Kornel, I realize you don't have an infinite amount of time to devote to this game, but it just seems like it is pulling in 2 opposite directions at the same time. I know a lot of your fans love Ao100, the unique weapons, and the more traditional Roguelike features such as switches that can turn a whole floor into lava, but those aren't the things that make your game stand out. The inherited limitation though from your source material is that in DooM there are only a handful of monsters to fight compared to a full on Roguelike (even the original Rogue had 26 iirc), and most of them only have 1 attack. There are a number of ways I could see this game growing though by departing a bit more from the source material:
More monster types not found in DooM but appropriate to the theme of demons from hell with a cybernetic twist (a hovering cyber-eye that summons more monsters to your location if you don't kill them fast enough?)
Upgraded versions of older monster types, with new attacks / behaviors (such as deeper level Lost Souls causing extra armor loss, deep level pink demons having a high chance of disarming your main weapon, cacao demons that can move through walls)
Invisible monsters (you can hear them with your RL's sounds but you can't see them until they are within "x" squares of you, and you can see where their projectiles came from)
Named monsters (like a palette swap from Diablo, sort of mini-bosses used to guard a supply [mods, healthpacks, ammo] cache)
Alternatively, another way this game could really grow without departing from the source material would be larger maps than the Nethack size, featuring generated puzzles as you get deeper in the form of 1-3 keycards and locked doors, though this would be even better if combined with the above "more monster variety" bits. You could also change switches to always spawn with the intent of lowering a specific wall as part of a puzzle to get to the exit (oh god please do this). Randomly generated levels are great, and by making yours more complex it would really enhance the experience on the whole. Since your game has no built in time limit (food, mutations, etc...) there is no reason not to embrace more spacious level design and monster behavior that takes advantage of it (patrols). This would also enhance the exploration aspect of the game.
As for what you've already got going right now that could be expanded on "easily", the weapon modding system you've put in is something not seen in most other roguelikes and would be a great part of your game to give more emphasis. It should be required that you use weapon mods in order to win the game, is what I mean by that, and thoughtful use of them required to win to win in the last 3 difficulties. This is impossible as long as you can just go into a special level and come out with a Plasma rifle with unlimited ammo, or a Missile Launcher that you can kite Barons of Hell with easily (well shoot even the normal rocket launcher is good at that). I know a lot of what I had posted in the dream notes looks like major buffs to the standard moddable weapons as a result, but I hid a disclaimer in there at the top "monster hp increased" to help maintain the difficulty.
I guess I would also add to the dream notes that larger monsters (arachs, knights, barons, mancubus, revenants, etc...) can't be knocked back by your explosives / barrels, or at least only have a CHANCE to be knocked back and not nearly as far. While I'm talking about monster behavior I believe a chance of "flinching" after receiving heavy damage may be a good way to keep non-knockbackables from completely destroying the player. Maybe a new weapon property "Stopping Power", which rates how likely a weapon is to force a "flinch" action in a monster would handle this nicely, and it is reflected in the source as you can "stun" monsters temporarily by shooting them.
Something else that could be really good for the game could be a skill based trait system, coupled with starting player classes and weapon families (I'll explain weapon families after this part). As in, instead of xp levels and picking stuff from a list, your skills get better as you use them. A quick and dirty example of what I'm talking about:
Medicine - You gain more hp when using a medpack and can self diagnose abnormal status effects accurately (game would need some abnormal status effects such as diseases / poisons for that to matter *wink wink nudge nudge*)
Maintenance - You have a higher chance of salvaging an upgrade mod from dismantling weapons, and can apply more mods to a single item (and dismantling weapons would be the only way to find mods)
Shotguns - Your accuracy and reload time while using shotguns
Handguns - Ditto, and, you can dual wield as soon as you find a second pistol in this system, but with an accuracy penalty (that is eventually overcome by 3-4 skill as described below)
Big Guns - Chaingun, Rocket Launcher, BFG
Rifles - Plasma, Sniper
Melee - Your accuracy / dodge ability in melee
The last five weapon skills are actually referring to entire families of weapons and how good the player is at handling them, which could be expanded to include more "standard" types (improved variants to keep up with the tougher new monsters) found as you get deeper in the complex.
Using these traits you could have player archtypes with beginning bonuses / predetermined skill caps (lets assume 2 is competent (no penalties, unless dual wielding), and 4 is the highest skill level for this example) like these:
Medic - Medicine 2(4), Maintenance 1(2), Handguns 1(2), Shotguns 1(3), Rifles 1(2) Heavy Weapons 0(1), Melee 1 (2)
Mechanic - Medicine 1(2), Maintenance 2(4), Handguns 0(1), Shotguns 1(2), Rifles 1(2) Heavy Weapons 1(2), Melee 1 (2)
Officer - Medicine 1(3), Maintenance 1(3) Handguns 1(2), Shotguns 1(2), Rifles 1(2) Heavy Weapons 1(2), Melee 1(2)
Sniper - Medicine 1(2), Maintenance 1(3), Handguns 1(2), Shotguns 1(2), Rifles 2(4) Heavy Weapons 1(2), Melee 0(1)
Skirmisher - Medicine 1(2), Maintenance 1(2), Handguns 1(2), Shotguns 2(4), Rifles 0(1) Heavy Weapons 1(2), Melee 1(3)
Heavy Weapons Guy - Medicine 1(2), Maintenance 1(3), Handguns 0(1), Shotguns 2(3), Rifles 0(1) Heavy Weapons 2(4), Melee 1(2), Sandvich 5(5)
Close Combat Instructor - Medicine 2(3), Maintenance 1(2), Handguns 1(2), Shotguns 1(3) Rifles 0(1) Heavy Weapons 0(1), Melee 2(4)
whew.. that took longer than I thought to write out those demo classes. Anyways this is just an extremely simplified class/skill system example that could be really cool.
