On tact boots: They're not the no brainer they used to be. I've largely stopped making them, just settling for a set of A-mod steel speed boots for the early game. The extra speed is of minimal benefit, I can live without the regen (repairing is good enough for boots), I get to keep the 1 point of protection on my feet (not great, but it is something if I need to run across some acid), there isn't the guarantee of the early A-mods from the Chained Court (so there's not the surplus there once was, making saving a second A mod much more tempting), and, of course, there's no dodging bonus now. I don't think they need to be changed. They're still good (the extra 5% speed is sometimes exactly what I need, so I have reasons to build them), but I also think about going with A-mod plasteel (or any other better boots I can get). So I think the balance is quite good, although some people might still be tact boot junkies out of habit.
That said, and to move on to the subject of mods... one of the big problems with S and F mods is that many PCs can't make use of them. Assemblies for the weapons that can't sue them helps a bit (I was surprised by PS/Plasmatic Shrapnel... I would have gone with an F assembly and the real life dragonsbreath rounds). But what pretty much guarantees a mod is useful is if it has a good use on armour/boots... there isn't a Naked Angel challenge or badge yet, so, other than personal challenge, everyone likes wearing clothes. Improving things along those lines would help a lot... suggestions like giving T and F mods the ability to boost resistances on armour is a good step in that direction. For S mods and armour/boots, I'd suggest the possibility that they do sort of the inverse of what they do on guns by granting "stealth" to make you harder to hit. Since mechanically that would mean dodging, that would allow people to build the old tactic boots by adding an S mod to them.
I think that pistols are just fine without a common upgrade. The other benefits from traits and mods make up for it. So much so, that that's another part of why I don't consider using MSc with guns... it's not much harder to build the twinky gun out of your starting pistol going masterless with just WK2, and then you still have the option to take DG for when you find the GCB. It just wouldn't feel like I was using MSc (and I think that's largely going to be the case with MSc in the big dungeons... it might seem like that's the place MSc should shine, but you'd have it backwards, large dungeons are where MSc will obsolete itself, and that will always be the case), and if that's the case, I might as well go no-master. The basic pistol development path is just that strong. It's also nice to know that you can finish the game with the weapon you start with... one of the things that's always bothered me with CRPGs is the trope where the hero character starts the game with some sentimental weapon like their father's sword, and ends up tossing it a couple levels later like it was nothing.
Not being able to really "use" MSv is part of it's problem, too. The use of it is too passive to really give a feel that you've gained much over no-master. Which is important, if you aren't actively using something then it's going to seem like that... I once started up a game and had a rough time of it until I leveled up and "discovered" that I was shooting things with a Bru3 Vampyre. Another time, I fought the Shambler twins with MGK, and proceeded to forget the whole "Kata" bit, and took an embarrassing amount of plasma bolts. So even if you do have a master, if you're not working it, it will never seem better than none. But that's only part of the Survivalist's problems, because unlike Scavenger, it doesn't give any offense in the skills required to build it. It also takes 6 specific traits... meaning that when you compare it to the somewhat similar Vampyre (in that both are good for being robust, with Badass and an ability to build overcharge as part of the trait), it comes up doubly weak (Vampyre has a lot of offense, and only requires 5 traits -- one of which is a wild card). Now, I can see a reason for having the tanking marine option available, but at the very least, the requirements should be lowered. I'm thinking -2 Iro and +1 wild card (ie require 5 traits like the other quick masters (which include MSc): Iro1, TaN2, Bad1, plus a fifth). The wild card is important (instead of just dropping 1 level of Iro)... it gives people the option to still go with another Iro, or to go with a Bad, or to take an offensive trait (or two because the master is quick to get). Another change might be to change the anti-requisite SoB to TH (or something else). Survivalist could make a decent rapid-fire build (becoming the heavy weapon guy), but having no access to the rapid-fire trait tree at all is a bit too much (especially since MSc at least has limited access). That's at least what I recommend as a start for reforming MSv.
As far as Juggler goes... splitting it into two levels is too much. It can still be improved without going there. The problem is largely that keybindings can be defined to give 'quick_command' access to any weapon, and that's not obvious to most people. So my suggestion would be to rework the whole quick key system so that the player can assign specific weapons to be juggled by assigning them to one of the ten quick keys. So instead of having "6" be "find me the most loaded chaingun", it would be "wield the specific weapon I've assigned to 6". Only weapons that are assigned would be able to be juggled, and any command to wield one (swap, inventory, mouse wheel, whatever) would cause juggling.