I dont know I'm just excited about the possiblities 
An Option to create "Your" character: At the beginning you could choose a race and maybe a skill for your captain. Perhaps you lose the game if your captain dies or perhaps not. Races could still be limited by ships.
Traits: Crew members could start with randomized traits that made some more valuable than others. Most of the traits would be combination good and bad, but with some that are only good, only bad, or extremely good.
Normal Traits:
Intellectual: Trains at twice speed, but 10% less health.
Pyro: 5% Chance to start fires when on enemy ships and attacking. However a 1% chance to start fires on your own ship when attacking.
Death or Glory: Takes extra melee damage and deals extra melee damage.
Trigger Happy: Weapons charge 50% faster. Small chance of damaging the weapons system.
Old Dog: Starts with some skills, but cant learn any more.
Computer Person: Gives an extra power bar in the drone room.
Territorial: Fights with extra effectiveness on your ship. Cant beam to other ships.
Bad Traits:
Frail: 10% Less Health, Less combat damage
Clumsy: When moving through a room, has a 2% chance to break the system.
Sick: Gradually Loses max health as you progress until dead.
Pacifist: Cant deal combat damage or man weapons systems.
Red Shirt: (This one could actually be useful) Whenever an event kills or takes one or more of your crew, this guy is one of them.
Good Traits:
Handy: Repairs at 1.5X speed.
Traveler: Can give information similar to long-range scanners occasionally
Squad Leader: Gives a bonus to attack to all crew members in the room with him
Super Rare Traits:
"Gifted": Gives the same abilities as the slug race.
Personal Teleporter: Teleport as individual. 45 sec cooldown
Tinkerer: Gives an improvement to the room they are in as if it was upgraded. (Need a level 2 Med bay? Stick em there)
Shield Affinity: Gives an extra shield layer if in the shield room.
Diplomatic: Gives extra blue options sometimes, often resulting in more peaceful options and extra volunteers. Can't deal damage or man systems. Has a low chance of converting a crew member to your side if in the same room for a time.
The Legend: Enemy crew will run away quite often when facing them.
As you can see this would make for some interestingly overpowered as well as almost useless characters. Like a pyro rockman or a pacifist Mantis.
Some sort of very small skill tree or something for more special abilities. Perhaps give skilled people the ability to overcharge systems for a time, or they use their understanding of that system to circumvent the opponents.
And maybe, just maybe, some sort of off the ship encounters. What happens with that away team you send to the research station? How do your guys fight those giant spider monsters? I think it would give a nice break from the ship combat
Also, when their are bigger ships, Fighter pilots. Fighters are launched out, and must be retrieved before you jump again. They are sort of high risk high reward weapons where you are putting a crew member in an expensive, fragile ship with only a high dodge chance protecting it. But extra weapons are always nice.
Anyways, this was just for fun, tell me what your ideas are!