On commercial engine sizes. I think it's rather doubtful mechanics now, that large engines need very large crews. It's some sort of coal epoch way of thinking: the more power, the more stokers you need. It's rather strange for space ship with nuclear power to have hundreds of crewmen to service it's engines, and even more strange to have linear dependence between engine power and crewmen needed. Is there any need to stoke nuclear fuel with shovels seriously?!
Not that it looks strange with engines only - it seems that cannons in Aurora are pointing and reloading with muscle power too!
So, there are 2 obvious problems with curent mechanics:
1. There is no mean to make commercial couriers, buisness passenger craft, something like traffic control craft and so on. And I think Steve have no desire to make it possible, because it adds some complexities for the AI and, in addition, it can slowdown any campaign very quickly, so it's easier to fully abstract such commercial smallcraft activity.
Personally I have to add some lore about aether storms, that makes smallcraft spacefaring too dangerous if you have no mil-grade engines and very good trained pilots, and so I use no couriers (even military ones) and no small patrol or survey craft too in my latest campaigs.
So, make small commercial engines possible - and it will be possible to make all these commercial smallcraft (small engines with nearly no crew and no MSP!) to populate our systems with auxiliary traffic and slowdown our campaigns. Well, it will be up to you, player, really, just don't whine in a bug thread afterwards.
2. Large commercial ships are way more crew-devouring that it can be plausible. It's rather plausible that you cannot automate detection and tactics (although it's strange therefore that your officer's skills adds no bonus to missile fire and detection at all) and hangar ops, but engine service?.. The biggest real commercial engines at tankers and even liners need only several crewmen to service them during nearly year-long voyages.
So, what I think is possible to optimize with commercial engines aside of fuel usage (ramscoop tech) to get rid of those special rules:
Make nearly all components to use crewmen in nearly static way. There is no matter really (plausibly) if it's 1-ton nuclear gun or 1000-ton nucler gun: you need 1 or 2 operators anyway, because they doesn't need their muscles to rotate and reload it, and mechanically bigger gun isn't more complex than smaller one to know how to service it onboard. So the biggest components possible may need several more crewmen then smallest ones just for redundancy of service for expensive toys, no more.
Both military and commercial ships will become smaller (and those players who love smaller ships - will have them), but the smallest ones will lose much of their advantages: they will keep most of their tactical advantages of lesser detectability, they will be still very potent at sensor picket and necessary in independent patrol (especially with new spoiler race on) or tramp roles, but it will be much less sense in making swarms of destroyer-grade battle ships or harvesters to sit in hundreds on every gas giant and so on. Less flags needed - less performance and micro burden and strange elusive bugs for average player.