I posted this 0.9.9.8 (and early 0.9.9.9 beta) build tier list on the JH Discord and was asked to post it here so I could include the short summaries I wrote explaining my rationale for each ranking.
This tier list factors how the build does at every point in the game and overall consistency, not just ranking on potential (what good is potential if you'll always die before reaching it or will almost never get the rare equipment you need for it?), nor how likely a build gets you past Phobos (sure Phobos is usually the hardest part, but Phobos deaths are much less painful than deaths in Deimos and especially Hell, so increasing your odds of not dying in Deimos and Hell is still important), and considers how much the build actually helps you clear difficult levels and survive arduous combat situations (any build can 100% clear a level without damage with a perfect corner shooting spot and a Tactical Shotgun, but rarely will you find such ideal conditions, especially on harder difficulties, so the less you have to depend on ideal conditions the better). Tiers are ordered, but the ordering isn't super important.
S tier
(Clearly broken and needs to be nerfed)
*Vampyre - Trivializes the standard game when it gives you near-IDDQD even in Angel Of Max Carnage and is by far the easiest option for most challenges/badges. Strategy with Vampyre also often amounts to little more than "run into enemies, mash click until they die", with maybe some rocket jumps in there to close gaps and calculated facerockets to trigger Berserker before rushing in. Its only weaknesses is a mediocre early game (that is mitigated with the free trait you get and being a level 6 mastery), and the Hellrunner block makes it not so ideal for any time-sensitive challenges, but it's so strong it could probably still work in those. The gap between Vampyre and every other build grows even farther on Nightmare, when melee is very powerful at corpse handling and Vampyre can abuse respawns for a full health refill whenever needed. It also requires nothing more than a mundane Nanofiber Red Armor and Chainsaw (or even just a Chainsword) to break the game, no need for rare or otherwise hard-to-get equipment, so it's super consistent and its floor is greater than nearly every other build's ceiling.
A+ tier
(Borderline broken, might need a nerf but doesn't outright trivialize the game)
*Ammochain - EE block makes typical rapid fire weapons unreliable and not being able to get WK1/2 until level 10/11 minimum without putting off Ammochain sucks, but consuming 1 cell per plasma burst is so powerful, both ammo-conservation and combat wise (other builds can't do more than five consecutive shots with a Plasma Rifle + TH2 without needing to go through a long reload or building a Nanomachic Plasma Rifle, while Ammochain can do 40 consecutive shots with a vanilla Plasma Rifle without reloading), and having Reloader makes Shotguns a very reliable fallback, while that in addition to the Marine's durability makes the early game easy too. Also has the uncommon ability to get both HR + Berserker to make it even more powerful late game, and its non-EE blocks are irrelevant. Overall has a very high floor with one of the highest ceilings (just needs a Hyperblaster to crush the game, while getting any of the rare mods, a Laser Rifle, or Nuclear Plasma Rifle sends it into the stratosphere), with few special levels and challenges posing any issue.
A tier
(Very powerful and often optimal builds, but have enough drawbacks to usually not make the game a cakewalk)
*Shottyhead - One of the strongest mastery effects despite its simplicity, while also having very strong prereqs, being able to get WK at a reasonable level, doesn't require ancillary traits but still retains strong post-mastery options like Berserker and Intuition, and has probably the easiest early game of any build. Its only stumbling is the SoB + EE block makes any sort of Plasma Rifle much less effective, but this isn't a big deal unless the RNG is very stingy with shells when you essentially got rapid fire shotguns. It has one of the highest floors with one of the highest ceilings, while being good at every point of the game and rarely being worse than a solid pick for any given challenge, but being vulnerable to ammo concerns without a Nano mod keeps it from the A+ tier.
*Scavenger - Essentially plays like a masterless build, but gets more mods than usual and a lot more of those very coveted rare mods, that combines very nicely with the Technician's inherent abilities. While luck dependent, it'll usually get better equipment than other builds around the midgame, and is far more likely to obtain the super equipment that will trivialize the game. While it has the fewest blocks of any mastery and two of the blocks are pretty irrelevant, the Berserker block is painful and can leave the build somewhat vulnerable lategame without good armor. Like masterless builds, it can also lack power in late Phobos and early Deimos before you get the aforementioned buffed equipment, but is usually no worse than solid for any challenge that doesn't require immediate power.
*Cateye - The best build at damage avoidance, while it also offers a level of flexibility not seen in most other masteries, and has a good effect that benefits any weapon type, making it more of a "generalist" mastery than the actual intended generalist Scout mastery. Can have the problem of wanting too many traits however (particularly being unable to fit Int2 + WK2 + EE + HR in a timely manner), and Cateye can be lacking in power when damage avoidance is not possible, which cannot be alleviated by getting Berserker either as it's blocked (which also makes the build more fragile in the lategame). Often a viable pick regardless of the challenge, and does have the particular perk of being brokenly good in Angel of Max Carnage.
*Blademaster - No other build can clear floors faster, and Berserker in general is very strong, while its power scales up the higher the difficulty as its ability becomes more useful the more enemies there are. Its early game is on the weaker end and the late Whizkid acquisition sucks, while its effect doesn't really do much against isolated enemies, keeping it from being broken, but it remains consistently good floor and ceiling wise, and it remains an optimal pick for many challenges/badges, or when you just want to rush through the game with more power than a masterless build offers.
*Masterless Scout - The unequivocal best stair dive build, and the ultimate flexibility combines nicely with the Scout's inherent abilities. For more complete playthroughs however, its lack of power in the mid and late game can hold it back in difficult combat encounters and harder special levels, and generally specialization towards something will be more useful for any challenge/badge that isn't a stair dive. Still remains A tier for its stair diving dominance and the fact you can never really go wrong with it.
B tier
(Powerful builds with their fair share of drawbacks that keep them from being top tier picks)
*Masterless Marine - Generally outclassed by Masterless Scout and other Marine masteries, which fulfill their respective roles better, but it still has the strengths of versatility in a masterless build, and has a strong niche when you need a bulkier build than Masterless Scout while also needing said masterless versatility (particularly if you want Hellrunner on something bulky, which all non-Ammochain Marine masteries block, without having to make a detour for Triggerhappy as Ammochain would require).
*Survivalist - It fulfills its role well as the tank build, at the expense of having the worst offense in the game and a painful Hellrunner block. Usually terrible offense would tank a build's viability, but Survivalist makes tanking actually viable and gives you a big margin of error to play with, allowing you to get away with repeated mistakes and bad RNG rolls that would be fatal for nearly any other build. The lack of offense and speed can still get it overwhelmed though, and it's bad for any time-sensitive event, which alongside being generally outclassed by Vampyre, keeps it from being top tier.
*Masterless Technician - Mostly outclassed by Scavenger if you want to make the most of a generalist Technician, and mostly outclassed by the other Masterless builds if you want to make the most of having no mastery, as the Scout and Marine have stronger innate bonuses (particularly in the early game). But as a masterless build it's still pretty good, and it does have the niche of a generalist Technician's advantages that retains access to Berserker (which is particularly relevant in Angel Of Humanity).
*Army of the Dead - Probably has the lowest ceiling of any build, with probably the weakest mastery effect in the game (aside from Entrenchment) that becomes irrelevant with Nano-Shrapnal and Plasma(tic) Shotguns, and is probably never an optimal pick for any challenge/badge. But it has a good early and mid game with Shotgun specialization, Marine's durability, and relatively quick access to Whizkid, while Shotguns never become bad and it can still spec into a Berserker sidearm to help in the lategame if needed. With a high consistent floor that depends little on equipment/item luck, this build is rarely an outright bad pick outside of any challenge/badge that requires Hellrunner.
C tier
(Functional but held back by serious flaws, could use a buff)
*Sharpshooter - One of the strongest mastery effects in the game, and thanks to Technician, doesn't need to invest in Finesse to get Whizkid, which is very useful for a Pistol build. As a result, it has one of the strongest mid games and a still impressive late game, which is also boosted by it retaining access to the Good Stuff to bolster it farther in the later game (with the SoB block being its only real painful block). However, due to Pistol specialization and awful prereqs, it has an absolutely abysmal early game, the worst of any build, which gives it an awful survival rate in Phobos on harder difficulties if you're not very good at the game, and makes it very unideal for any challenge/badge where early power is needed. Such a polarizing mastery can be hard to rank, on a pure winrate basis it would be possibly the worst and generally Phobos is the hardest part, but since Phobos deaths are much less punishing time-investment wise, a build that offers such good mid and late game consistency still has value.
*Gunrunner - Has one of the highest potential ceilings in the game, being able to effectively get Pistol firing rates on Shotguns and Rocket Launchers while firing/moving/reloading all at the same time, and any combination of HR + Fin + Rel gives it an easy early game. But this mastery requires significant ancillary investment as it needs Shottyman to actually do anything worthwhile, which combined with a very late Whizkid acquisition and requiring the generally unhelpful Dodgemaster, gives it a very weak mid game. Gunrunner itself can also be rather finicky to utilize and is very ammo hungry whenever you use it, while the Brute block prevents you from effectively using a melee backup, as well as leaves you always frail. It can feel very good to wipe out a nasty horde in a quick run rampage, but deaths in Deimos are always painful and Shottyhead generally outclasses it (which you'll need to actively forego as you build to Gunrunner + Shottyman, as it overlaps Shottyhead's prereqs).
*Fireangel - Its defensive benefit is potentially very handy and no-damage rocket jumps is a nice benefit, but it offering no sort of offensive boost, while also blocking SoB and EE, leaves it with one of the worst offenses in the game, and the defensive benefit is not so good as to be worth the tradeoff. It has a tantalizing ceiling with being able to blow up everything with the Mother-In-Law, Nanomachic Tristar Blaster, or a nano-modded BFG 10K with no risk of blowing yourself up, but you'll very rarely get such weapons and often won't even get a Nano mod just to build a Nanomachic Rocket Launcher, which is necessary to take extensive advantage of rocket launchers offensively since rockets come in such small ammo quantities. It retains access to Berserker to compensate for the lack of offense, but besides not being easy to fit in, Fireangel removes the ability for you to get Berserker procs off of facerockets and barrels, making it not as strong as Berserker is in the hands of other builds. Overall it's not that bad, and has a decent early game thanks to Shotgun specialization, but it's never really any good either, outside of a particular niche with the Gatekeeper badges.
*Malicious Blades - The mastery effect is decent, but its offensive and defensive benefits are almost entirely outclassed by those of Berserker, which it blocks. The mastery has the benefit of its defense-boosting effects being usable with non-melee weapons, which when combined with it not blocking SoB like the other melee masteries, allows it to function more effectively as a hybrid-melee build, but such a build requires a ton of traits that leaves it weak for a long time, and having to keep a blade in your prepared slot to get said defense-boost prevents you from utilizing ammo boxes, hurting it farther in a hybrid build. Whether as a pure melee Technician or hybrid melee build, you are better off going masterless and getting Berserker instead, and a build specializing in blades specifically would still do much better with the other melee masteries. I don't see any challenge/badge where this is a remotely optimal pick, but it's never bad enough to rank it in the lower tiers.
D tier
(These builds aren't unplayable, but they're severely flawed and using them makes the game much harder, in need of significant buffs)
*Gun Kata - HR investment gives it a slightly easier early game than other Pistol masteries, but investing in Pistols still gives you a much harder early game compared to non-Pistol builds (and ultimately with pistols, you would rather stack SoG with SoB and get a level of EE early rather than get HR, as getting your combat to something acceptable is of upmost importance, so Pistol builds that don't go with any Pistol mastery still have the least painful early game). Unlike Sharpshooter however, it requires several ancillary traits to be effective; it technically doesn't require SoG3 but you need it ASAP or else your Pistols don't do shit, making Gun Kata effectively a level 8 mastery, but you also need two levels of Fin before you can get WK that's desperately needed for Pistol builds, then you need SoG 4 and 5 after that, still really want at least one level of EE so you stop missing so much, and you would want to fit in Int too... The SoB block without Sharpshooter's guaranteed max damage also makes your Pistols quite weak and unreliable, at least before you get SoG5, or before you get a Unique pistol or an Exotic pistol maxed out with Power mods. You altogether get a build with a weak early game, an abysmal mid game, and a still unimpressive late game, so you're always lagging behind other builds at every stage of the game. Gun Kata's effects itself can also be rendered pointless, as the "shoot faster after dodging" bonus doesn't matter once you reach the firing speed cap (nevermind the unreliability, if not outright impracticality, of utilizing it in typical difficult combat scenarios), and the reloading bonus doesn't matter if you get a Nanomachic Pistol or a Blaster (while being a finicky effect to utilize in general, especially compared to just using one Pistol and an ammo box). If you want to use Pistols with a Scout, you're better off going masterless or even Cateye, which doesn't block SoB and has an effect that is always useful regardless of what Pistols you have.
*Bullet Dance - It has theoretically the highest DPS ceiling of any build, but similar to Gun Kata it requires a grotesque amount of ancillary traits, while having the "Pistols suck in early game" problem exasperated by having to pick an actually useless trait in Triggerhappy, and Bullet Dance itself does more harm than good unless you find a Nano mod to build a Nanomachic Pistol or find a Combat Pistol and bulk mod the crap out of it, which you often won't. Said DPS ceiling is also rather overkill, when a Pistol with SoG5 and several levels of SoB will quickly kill anything before they can retaliate without the ammo-draining drawbacks of Bullet Dance. So you get a very weak early and mid game, for a late game that usually isn't all that hot either. If you want to use Pistols with a Marine, you're again better off going masterless, as you don't need to pick up Triggerhappy nor bother with Dualgunner until it's actually useful, while retaining freedom to get HR and even Berserker if you want extra lategame assurance (particularly in A100).
E(ntrenchment) tier
(Outright sucks, in desperate need of serious buffs or being overhauled completely)
*Entrenchment - Has awful prereqs that makes the early game hard, Finesse block cripples its offense with any weapon, requires a lot of ancillary traits that gives it a very hard mid game, all for a very underwhelming purely defensive mastery that both only kicks in when Chainfiring and gives resistances that are only slightly better than the resistances the Marine has inherently at all times. Then for the cherry on top, if you actually try to utilize it extensively, you'll waste a lot of ammo and quickly empty your clip, where you're then stuck with having to reload weapons that have 2+ second reload times while no longer having your resistances and not even being able to get Reloader to lessen the mauling you'll suffer. So you need to either find a Minigun and tons of bullets, or a Nano mod to make a Nanomachic Plasma Rifle, just to make the build even functional.
