I'd be really careful about radically increasing the %age of space devoted to non-combat systems. Push it too far, and you'll make expeditionary warfare essentially impossible. You'd end up with 2 schools of design, System Defence (ships for local defence only, spend 98% of their lives tied up alongside port, tiny fuel and maint facilities, only ever go into space to fight an observed enemy) and Expeditionary, with the legs to take the fight to an enemy and patrol, but badly under-armed / armoured for their weight, comparative to current designs.
I also suspect that for Expeditionary designs, you'd be forced to take a very specialised division of labour approach to ship / fleet design, with dedicated sensor platforms, PD platforms, missile / beam platforms etc. Except at pretty high tech levels, ships capable of independent action would become nearly impossible to build. Parasitic weight penalties get big, fast
Increasing fuel consumption of missiles significantly would have pretty dire consequences for that aspect of combat too. For a given size of missile, you would have to give up range, warhead, agility or speed (or a combination), so missiles would either become less capable, or much bigger. In either case, PD would become proportionately much more powerful.
>> Starbase
>> There needs to be some plausible reason why it doesn't work with engines that also maintains internal consistency within the game.
Borrow / adapt the SFB "positional stabilisers" concept. You need one to make the maint component work (and possibly other things too, like allowing faster missile launch rates), and it disables engines, because your position is stabilised
Size 1 AMMs wouldn't suffer much, because they barely carry any fuel anyway. Going from 0.005 to 0.05 MSPs of fuel is nearly insignificant, and leaves you with nearly as good an AMM as you have now, against much worse, or much more expensive ASMs. It would certainly make ASM armour, and 2 stage missiles much more attractive though.
As for crew, what I think you're reaching for is a crew comfort score. In a fighter / FAC with a limited deployment time, crew comfort is a low priority, people can hot bunk and eat off their knees for a few days at a time, with no real adverse effects. For extended survey cruises for example, which may mean being in space for years at a time, crew would need more facilities to keep their edge. Overprovision of crew quarters (representing individual rooms, and private space), dedicated leisure areas, dedicated mess and galleys, hydroponics areas for fresh food, not Navy concentrates every day... This is what keeps survey crews sane and functional.
Run it as a "Crew Comfort Timer", similar to expected maint life. If you exceed it, morale / efficiency drops (presumably expressed as a temporary drop in crew grade). As you add more space for crew comfort, the timer rises, allowing longer deployment times with 100% of nominal crew efficiency. If crew areas get trashed by battle damage, you may have to send a ship home for repair even if its combat capable, because the crew are sleeping in corridors and the engine room, and living off unheated rations