Doesn't this new system cause priority to play 'double duty' for ship repairs and crew distribution, something that may be unfavorable?
Supposing I had an awesome dreadnought, a secondary combat ship, one or more ships I captured that I'd want to tow around but not ever use, maybe some fighters, and some sort of cargo hauler. Some or all of these ships are lightly damaged. I use a lot of my crew capacity for marines, in case I ever run into a cappable onslaught or something.
The awesome dreadnought got severely damaged, but I don't want to lose it in combat, so until such a time as it's repaired, I don't want to field it in combat at all. Therefore, I don't mind it being undercrewed, because I need my secondary ship fully crewed - but I /do/ want it receiving repairs, at maximum priority, because when it's fixed I'll be fielding it in battle.
Currently, if you want something repaired maximum-fast, you also have to designate it to be fully crewed, which may not be an option if you don't want to fly damaged ships into combat (because you have other ships). This is especially a problem if this damaged ship is vastly larger than the other ships in your fleet: Otherwise you'd be able to field a bunch of smaller ships, and maybe skeletal-crew this one, but as is, all your crew are sucked into the dreadnaught leaving you far fewer ships you can field in combat.
With this you could argue 'But Bob, you have a high crew capacity with this supposition! This shouldn't be a problem!' Okay, then I present this: You used a bunch of smaller ships to defeat and capture a large capital ship of awesomeness. You use most of your personnel capacity for marines, to ensure this can happen. You want to field this giant ship as soon as possible, because it's giant and awesome, but you need your other ships to be crewed in the meantime so you aren't flying this damaged husk into battle. You can't just let it sit at the back of the line for repairs, because your other ships were somewhat damaged too, and you really want to repair this big ship before getting to the rest of them - once you do, you won't need the smaller ships anymore. What do?