Two thoughts:
1) Would you change the size breaks for fighter/GB/Corvettes (bridgeless ships) etc? I was originally going to say you'd need to up the threshold for bridgeless ships, e.g. to 1200 tons, but while typing this I realized that the other way to go would be to introduce fatigue rules: the difference between a fighter and a frigate is that the frigate has ~3x the crew-per-system that a fighter does, and that the frigate has crew quarters. So to get away from the arbitrary 1000-ton discontinuity you'd probably want to set things up so that if the crew, on average, is on duty more than e.g. 40% of the time (which is a bit higher than 3x but a bit lower than 2x) then fatigue levels begin to rise. Similarly, if the crew doesn't have enough "resting space" then the fatigue levels also rise. So for a fighter you just need 1 shift of crew and a place for them to work at their station; for something like a gunboat (i.e. short duration littoral warfare) you'd need 3x crew per station but only 3x (or even 5x) the space (which would induce fatigue levels to start to grow after a few days), and for a frigate (i.e. blue water, arbitrarily long deployment) you'd need 3x crew and 5x (or even 10x) the space.
2) This has the potential for a LOT of micromanagement, both at the design level and at the operational level (if you introduce fatigue levels). In essence you'd be re-introducing readiness states if you go with fatigue rules, and the fatigue rules are what I think make the crew quarters change worth it. Similarly, you already need to pay a lot of attention to fuel in Aurora if you use GB/FAC and/or fighters - I'm a bit concerned that requiring even more planning would lead to the same sorts of problems we saw with maintenance. It certainly shouldn't be the case that a tanker uses 70% of the fuel on itself during a deployment, nor that a carrier can't refuel its fighters from on-board resources (which is almost the case now). Although maybe that means that fighter/FAC combat radii would go WAY down and we'd get as big a tactical shift as when you introduced realistic missile engines.
So I'm torn. I don't see a lot of need to disrupt the current game playability balance just to make crew quarters bigger. OTOH if you put in fatigue that would put a real continuum behind things like the readiness/surprise rules in SF, and the "Below 1000 tons you don't need a bridge" rule in Aurora.
John