I used to feel this way as well. I thought having crew represent the health of a ship was an unusual choice in the first place, and if it is in fact the "health indicator" then the idea of it affecting different ship functions would make perfect sense. I can't think of examples off the top of my head, but there are certainly other games that have applied a similar "crippling damage" gameplay mechanic. The idea of a ship being less effective as it takes serious damage definitely has merit and would an awesome addition.
Would be cool to have both a crew element as well as a hull armor and shield element a bit like the Protoss in Starcraft; shields can regenerate but once depleted, armor starts going down and doesn't regenerate, and once the armor is gone, crew start dying which in turn begins to cripple different parts of the ship and you slowly become a sitting duck as your destruction becomes inevitable.
The race diversity bonus has merit too. Master of Orion was a pioneer in race-augmented stats which made different species more adept at certain things than others. This is something that should be so easy to translate into Star Control. For example, a species like the Yehat have a naturally inate sense of flight so they could help improve your ship maneuvering tech, Umgah are bioengineering geniuses so they can help heal crew more rapidly or make them more resilient to damage, etc. You could go on and on with this.
It would be nice to see other mechanics added as well. This may have already come up in other threads, but one that springs to mind is a little more resource management. In SC2 all we had was fuel units as our primary limitation. Without getting too far into the "strategy" realm, I think it would be interesting to have other resources like food and life support energy so that you aren't handcuffed to a single resource.
If you run out of food, you would have to scan nearby star systems for organic compounds to harvest so that you could synthesize food. Maybe certain types of minerals that you mine would be compatible with the life support system and could be used to keep you going. It is too early to know for sure, but I sense that Stardock may be aiming to emulate the feel of SC2 where you go find resources and then return to home base to refuel and resupply but I think that's outdated and feel it would interesting to incorporate the ability for players to stay on the go by actively seeking out raw resources they can use without having to return all the way back home just to process them into generic resource units.