I like what you are saying about the carrot and not the stick but the only thing that comes to mind is smaller craft. I play on a server with a pretty low block cap (keeps fights from getting overkill and unbalanced) and adding a crew to a lot of the designs would require a lot of extra space that is not available. I always think back to so many rpgs where you as a player would always stack buffs even if you did not need to. Adding a pure carrot would just mean that crews are just another "plus" to the stats of a ship. No player would skip out on even the smallest boost which is just another added thing you need o be "competitive".
Maybe there is a sort of rimworld esque angle where you attract crew members instead of hiring them.
Though I will say I like the idea of a tactical officer calling out missile incoming warnings, or the likely destination of a ship that just jumped. Then there would be a nav officer as you said that acts as autopilot. The weapons system operator gets tricky since we have ai modules already. An engineer could redirect power, but why can a computer not do that too?
Well, there were concepts where the number of crew members you could have were limited by the size of your ship's crew quarters. Which means, the min/maxers would have to ask the question "Do I want the convenience bonuses crew give me (autopilot, auto-jump recharge, auto-targeting) or should I rather dedicate that space to more guns/shields/other systems?" I'd rather imagine crew roles as "You're not alone on this ship, you don't have to do everything yourself" as that's supposed to be their job.
Also, the big difference between a crew gunner and an AI module would be, a crew member assigned to his/her post (let's be gender equal here) would be active even if you're in control of the ship (from core or proposed captain's chair) while an AI turns off the moment you hop in the core. Also, no single crewmember could control your whole ship, just the stations they are assigned to.
I still think crew experience should be a thing. For example (possible commands in bold):
- A rookie navigator would only be able to
Recharge jump drives after a jump. He couldn't (and let's face it, since he's so green, you wouldn't want him to) meddle with the actual warp calculations
- After he watched you fly around for a while (open to debate how long) he learns to
Execute next jump to waypoint when you give him the order (because he was watching and learning)
- As he gains experience and you trust him a little more with your ship's systems, you'll let him control the sublight thrusters, and he'll learn to
Approach selected target , which would mean he'd fly the ship to the entity you selected with F, and keep a fixed distance from it (say, 300 meters. That's supposed to be enough not to crash into planet gravity) and attempt to follow the target if it moves.
- Finally, when he's a seasoned pilot and attained the skills expected from a trained navigator, he can Jump
to waypoint all the way with repeated jumps, instead of only being able to execute one jump in the chain at once.
Just like that, a Gunner could first only handle simple weapons (cannons, beams, dumbfire and heatseeker missiles) with mediocre accuracy and unable to lock the guided missiles, and only targeting the first detected hostile. As he learns, he would learn to get a missile lock, his accuracy would improve (like when you increase AI difficulty) and he'd be disciplined enough to attack your selected target, not whatever he sees first.
A Tactical Officer could slightly reduce cooldowns on your scanner, or automatically ping it every time it's up, maybe give you a warning if you're locked on by a missile launcher, and slightly reduce cooldown on your jammer and/or cloaker if it's dropped by a power failure or a hostile scanner. Alternatively, if we don't want crew only to give flat stat bonuses, he could target the ship that's locking onto you/scanned you/uses a jump inhibitor (with a different colored HUD indicator, like missile lock is yellow, this could be pulsing orange for example)
An Engineer could help with damage control if you get beaten up, able to perform a Fast reboot (15 seconds instead of 30) or an Armor Repair (previously only at shops, but this would take also 15 seconds) and on a maxed level, he could reduce the time you need out of combat for your shields to get back to full recharge.
Basicly, crew should be more of convenience, and less about raw stats.