Star Control was unique for using crew in stead of shielding or hull damage as a means to determine when your ship exploded.

I think it would be interesting to expand on this with crew management, such as:

1) Crew placement: Set the percentage crew on weapons, helm, engines, science stations to influence ship damage, rotation, speed, energy regen. When a particular type crew dies the efficiency goes down a bit. The ship remains operational as long as 1 crew member is alive; all other systems are taken over by AI. AI tech upgrades will lower the loss efficiency.

2) Explore the universe to recruit crew of different races. When the crew is of the same race as the ship, it gains a bonus on efficiency. Certain rare and unique races may give additional bonuses. Cloning tech can help increase certain crew types. --> Story arc: Cloning of hybrid races.