I was either using an old version or was just remembering wrong regarding the regenerating ammo, so that complaint was either moot or mistaken (if so, my apologies).
My complaint regarding the boss fleet is that I felt penalized for hitting level 30. All of a sudden I have to worry about some uberfleet constantly breathing down my neck. I'm not expecting a reward for leveling up; I am just expecting not to get punished for it.
Seeing that hull/armor was reduced for the bigger ships sounds nice. I felt most of the normal ships were okay, just the higher-end ships were not vanilla-balanced. I don't see myself using it as long as a boss fleet like that is a constant menace for reaching level 30. Just because a more skilled player can beat the boss fleet with one ship doesn't mean that it's vanilla-balanced.
Edit: I suppose to clarify: there are certainly similar 'boss fleets' in Uomoz that I generally don't like too much, but in that mod they are a) easily avoided and, more importantly, b) temporary. They're an optional challenge instead of a looming pain.