I think no one really wants crew tetris back, but more of a permanent 'battleworn' ship effect, maybe tied to crew for more RP purposes so as not to just think of it as an 'elite-level ship'. Crew cohesion sounds pretty nifty and would work on paper, the stability of the crew, maybe tied to commanding officer switches, number of battles/kills, whether it got damaged or disabled or had crew killed off, or just time spent across the board. But giving it a flat bonus would be too gamey and we have enough of those as is.
Maybe positive random event bonuses? 'The crew's night off ended up in an extra shift as they pulled together to fix the aft thrusters. 10% CR repaired (boosted above max if at limit)'.