If you want sensors to be more useful then have them extender the ranges of adjacent weapon systems or produce a 'data pack' resource that when placed increase weapon ranges, and missile turn rates.
As for missiles has anyone though of stealth missiles and giving them a better evade bonus.
You could make invasion missiles that don't explode but drop a drone off in the opponents ship to disable rooms and kill crew.
Nuclear/Fusion missiles are not all that effective in space explosive wise but the fact that they would produce an EMP, and radiation poisoning would be their only saving grace, other than a slightly better boom but the boom would be the same as the explosive might of 1.5 current missiles.
Radiation, and EMP should bypass shields with EMP having a random field size but radiation having a rather significant size.
Dedicated EMP missiles would have better randomized field sizes and only disable the things they touch. I thing this would prevent EMP damage from being op but still viable as a weapon choice.
Extinguisher stations should become your general purpose 'Deal with this' station.
Need an Extinguisher? go the the supply room.
Need tools to re-enable a room? Supply room.
Need to remove intruders? Get a gun at the supply room.
Cleaning radiation spills? Supply room.
And so.
The PDs should be an above hull 360° turret that uses a gay at 5 shots a second, 1 damage a short, 1/2 chance of hitting. This allows PDs to be more effective up close as high speed rounds miss less frequently... And travel time on the projectiles with collision detection on missiles, drones, and fighters only.
Shots per power cell should be 10-15 which means new cell every 2-3 seconds.
You could also introduce a FLAC PD that uses ammo instead of energy and has an aoe that hits 3/4 of the time. The projectile would travel slower than gat rounds.
Another PD idea is Chaf that is launched from the missile tubes.
Rooms disabled by EMP should be in the same state they were in before they were disabled so if a shield emitter is disabled with full power it shouldn't loss that power when it's fixed.
I may have missed a few things but that is the gist of what I got right now will post more when my Muse disides to work.
Edit: space mines! My muse has spoken. There is a suttle beauty to laying a trap for an unprepared foe. No propulsion stealth and bigger boom (3* current missile damage)