Sounds cool but has 2 flaws:
Stealth: i dont understand your idea. The Crew of the Enemy ship probably runs around all the time. There is no way they wouldn't notice the intruders. (Maybe they could have some sort of invisibility)
Micromanaging: It's ging to be really hard to manage all the crew + your own ship (possibly even a fleet). You would need a lot of pausing to do all that. (Maybe you could just assign a Task before the operation and after it has started it becomes unchangable and the AI just controls the crew)
I really like the idea with the random based combat System. (i have a pictures of X-Com in my mind where they just miss 3 times with a shotgun point-blank XD)
