Here's a list of things I want.
1) Fixed bugs of course. Mainly performance-wise, playing with more than 10 people is laggy as hell, playing with 20+ is impossible: with that many people I often die trying to switch o2 tanks for example. Having several vessels in close vicinity also kills FPS. Other common annoying things are shitty selection which jumps around when submarine moves, bugged movement between subs/shuttles where people see themselves teleported around while actually being stuck between the two, subs or people getting stuck in the rock after heavy impact and having to be teleported outside. At least Nilanth' mod mostly solves desync issues.
2) Add charge_out and set_charge_rate slots for batteries - right now many subs (Torrent and Underseeboot off the top of my head) have problems with fires/overloads when staying still - all batteries fully charge and grid load sharply drops. Giving sub makers ability to slow down charging as charge approaches 100% would help a lot.
3) Make fixing things take time, similar to using wrench on items attached to walls. Make time depend on skill, maybe allow everyone to fix everything but so that engineer could fix junction in 5 seconds and doctor in 5 minutes.
4) Only display health above creature's (including people) heads when wearing medical goggles. Do not show nicknames and healthbars through walls and floors.
5) For traitor rounds - after round ends let people vote on who they think traitor was - if most guess correctly traitor loses, if they don't traitor's kill is considered sneaky enough. Maybe it'll give some motivation for traitors to kill only their designated targets instead of literally everyone.
6) Make effect of things differ between people and aliens. Being able to stun derelict shuttle with a stun baton is the most absurd example, but I mean other small things like the fact that apparently same drugs have same effect on humans and aliens. Maybe make aliens immune to morbusine and chloral hydrate but susceptible to some things like iron powder or ethanol or some other benign substances? Maybe even randomize weaknesses each round so people have to experiment on aliens to find out effects.
7)Nerf stun weapons. Stun baton shouldn't work on people in underwater suits, and have smaller chance to work on people in jumpsuits. Chloral hydrate's effect should happen after some time instead of instantly. Right now all combat between players revolves around who can stun who first and insert a welding tank into their suit.

For singleplayer:
1)Make NPCs smarter, right now they get stuck even in default subs (e.g. next to medbay on Aegir mk3), on non-default subs they press buttons they shouldnt and it often kills them (e.g. button in airlock which closes door they just passed but also opens door outside and they get crushed), I cant make them carry this or fabricate that, so I have to spend half the round picking up stuff I bought in shop from the floor, making shells and fuel rods, they cant switch fuel rods, they cant fix junctions, they cant fix engines, they cant shoot farther that 2-3m away which often causes explosions to kill the shooter, etc. The only way to play game is to lock engies and mechanics in some safe room while you pilot ship and control one of them if something happens.
2)Make shells cheaper. Right now shells cost more than some of the easiest missions bring, kill missions are basically a waste of money since you're guaranteed to shoot more money than you'll get. After the battle I have to swim outside and search for shells to make ends meet.
3)Allow to sell items. After exploring ruins I get artifacts, shards, guns, but I have no use for them. Alien guns cannot even be used as nukes now, not sure if that's intentional or a bug, since in 0.6 they could be shot.