It's not a penalty. You gain PPT and CR recovery time. You also don't need to carry additional crew if you dont want. For fleets that want additional crew, but not the extra costs, crew transports could be used. So ships, whose main purpose is passanger ferries, wouldn't have a supply increase.
Well it's a penalty or bonus depending on whether you want more PPT/CR, or cheaper repairs. I'm worried those two things will counter each other out fairly handily, and make the whole system moot, OR one will be preferential to the other at which point it's just a min-maxing thing which not everyone enjoys.
Also I don't know how crew are split across ships in your fleet, but I'm pretty sure it's fairly low-brow. I don't know if the method of "bring dedicated crew transports" would work as well as you think, but I could be wrong.
Considering that crew-heavy ships are already giant cash sinkholes, it would only get worse with these changes.
Cruisers and capitals are already way too cheap to field and capitals really should only be affordable to a player once they have colonies to support them...
That's definitely subjective, but I'm a really slow player, and
I think that's over the top for limiting the player's progression. Also not everyone plays with colonies. Cruisers and capitals being too cheap is a more foundational balance issue, not something that should be solved with a concept like this (and probably not by making frigates and destroyers better). Also I don't think cruisers and caps are too cheap for what they do, but hey, what do I know? I'm just a guy who enjoys wrecking stuff in a player-controlled destroyer.
... Also, no additional costs if you run with a bare minimum crew compliment.
... I'm not convinced. There is a genuine penalty for having below minimum crew. You get in one fight, you lose even a handful of crew, and now you have less total CR. The min-maxers might adore this, but again not everyone plays that way. I'm not a min-maxer, and I'm certainly iffy about it.