So here are my suggestions:
1.) The veteran crew roster.
This is a list of survivors from previous games. This would be unlocked the first time you beat the game. When you win a game, the whole surviving crew goes here. When setting up a new ship in the hanger, you can swap out some of the ship's default crew for crew from the veterans roster. This means you could give yourself a leg-up by swapping in veterans of your favorite races who already have good skills, but in doing so you'd also be risking their lives a second time.
The most basic form of the veteran crew roster would be super simple to implement as well - just have a place in the profile to keep a list of crew member stats, and add the GUI needed to allow swapping them in.
If you wanted to get fancy, you could add more ways of sending crew members to the veteran's roster without beating the game - an escape pod that lets a single, beloved crew member escape a doomed ship, for instance, or the option to "chicken out" if you should limp into sector 8, but know full well that your ship is in no shape to face the boss.
Why is this Awesome?
It is an incredibly simple way to add a lot of depth and replayability - just by allowing crew and their stories and statistics to transcend a single play-through. It allows that attachment to grow between the player and the
2.) Captains.
The only way to get a captain should be to win the game - when that happens you should get to pick one crew member to be promoted to captain. Captains would have a little something extra compared to normal crew. They might have some other small personal advantages - a bit more HP than usual for their race, or an ability to get just a bit better at normal crew tasks - but the main advantage of a captain should be a unique special ability determined by their race.
Of course you can only take one captain on your ship when you start a new mission.
Why is this Awesome?
Every ship needs a captain! And truly iconic Starship's all have an equally iconic man or woman in command. Not only does this provide more progression for your veteran crew, but it gives the game more variety and replayability because of all the cool combinations of ship and captain that there are to try.
Here are some ideas of special abilities for captains of different races - of course they could be anything; this is just what I was able to come up with:
Human Captain - Charisma: +50% exp gain for all crew in all areas of experience.
Zoltan Captain - Contributes 2 power instead of one to systems in his room. If he is piloting the ship, this power is added directly to the reactor.
Rockman Captain - 35% Chance to prevent system damage to the room in which he is stationed(hull damage still gets through).
Mantis Captain - You can teleport through enemy Zoltan shields. Your teleporters can retrieve your crew from an enemy ship even if it is cloaked.
Android Race Captain - Can remotely repair any ship system (at half speed) from the bridge. (this could be an active ability button, like the crystal crew power, that is only active when in the pilot room).
Slug Captain - Your ship's sensors are immune to nebula interference. Slowly regenerates his own health no matter what he's doing?
Crystal Captain - Wasn't sure on this one. Maybe he always knows the way to the secret sector.
Thanks for reading!