Yeah, what I'm saying here, to clarify, is:
1. I have zero problem with the "player ships" being outsized in power, up to a point.
Really, the most fun in this game's combat is almost always little ships, not hulking behemoths.
I think the CR system, while imperfect, is largely doing what it needs to, in terms of limiting the player there. I think it goes a bit overboard, honestly; in late-game, with huge fleets on the battlefield, there is no way a player's taking down the fleet solo in even the most-egregiously-OP ships without chain-battling (and even then, it only works at all because player ships can be consistently faster than Fighters).
2. I think the issue with late-game fleets is largely as Plantissue points out: when we're limited on ships in our fleets, it becomes irrelevant if, say, 50 Wolves with leveled Captains can destroy 5 Onslaughts (they totally can, btw), because we cannot field 50 Wolves, even if DP allowed, because we're simply not allowed to have that many ships in a fleet. I was reeeeeeally glad to hear that we're going (back) to a soft-cap for this in the next major build, and frankly, I don't think it should even be done that way... but that's another topic.