Overwatch/readied attacks, for you and for enemies.
Nerfed bursting; it should be good but not as good as it can currently get. ARs should have a close-range penalty (maybe an option for a short-barrel) and narrower burst cones. I think this is the last real weapon-type rebalance that we need.
Baseball bat(s) and/or better crowbars.
I personally preferred the game not having a map, though im okay with the black sea having one.
More reason to play characters with both ranged and melee weapons, also the ability to quick-draw a knife or pistol, or to have gloves not take up slots. Really I just don't like the two weapon slot system as it is.
Shields you equip in a weapon slot; shields should have some defense versus ranged attacks (the tacvest/riot armor dynamic isnt so great in practice, so let's shake it up).
Lower item qualities after the early game.
More randomized quests/dungeons/maps/item, trap, and enemy placements.
More water maps/dungeons (like a shipyard, a native village on stilts, caves/tunnels, sewers, etc where you would make good use of jet skis).
A minigun.
Unique siphoner/ancient rat overcoat sprites, also everybody hates the sleeveless stealthy leather. Antithermic tacvest isn't a banger either.
The game simply isn't challenging past lvl 25ish, even on dom; maybe capping levels at 25 but allowing a few more feats and skill points would be better (with the regular cap of 135 on skills).
Improved (ability score) feat can only raise an ability up to 16 max.
Higher skill check caps in lategame.
Disassemble should include its spec automatically.
Grenadier should only be as strong as it is *after* specs.
Contraction ought to be a feat that requires 7 will (or something); its just too strong.
I want to explore Omega station.
More environmental dangers, like dungeons full of toxic or cryo gas, entire floors of fire, etc (we're getting more of this over time), also more really dark areas.
Trap rebalancing/nerfing; too many ideas for this to list here.
DC needs to be harder and/or randomized; last boss fight needs to be much harder, at least on harder difficulties.
DC random encounters, more black sea random encounters.
Gun nut grants another enhancement slot instead (bowyer too?).
The ability to improve or add to unique weapons someway (at least some of them anyway).
Randomized arena combatants (a pool of 3-5 for each tier).
Extra emphasis here: deeper dungeons with more nested areas
Plenty of ability checks/secrets/multiple routes (we've been getting more of this too).
Arena mode: play against other players in various arenas with various rules.
Co-op mode: run through the game or small side campaigns with a friend or two.
-A way to free the rejects from the Institute without turning everyone hostile.
You can do this. Also I like your list.