this started out with you saying that reducing the impact of skills would make everything into one-ship-vs-all
Because if we don't have fairly heroic Skills for AI Captains, then we're back to
player skill being the deciding factor, basically.
AI Captains are more of a liability than not until midgame; after that, the player can afford to take ship losses, if needbe, to get them the XP they need to hit higher levels.
If player skill, rather than stats, is what is most efficient, we're right back to the single-player-vs-all model of gameplay.
If you want fleet combat to be the normal way play progresses, then Captains make the difference between just soloing with a series of Medusas and rolling around with a mixed bag, tbh. Until Captains were a thing, I only used AI ships that could tank or be support; Captains made them viable to actually get them fighting. The problem isn't, "Captains are OP"... again, the problem is largely, "there is nothing challenging a player fleet built by a good player after about Level 30".
So, no, I don't agree about nerfing Skills; instead, make the high end much more challenging.
Otherwise, we're back to, "do I use the the Tempest or the Medusa to Solo All", because player skill vs. the AI is always going to go in the player's favor, at the high end of play. I think that the right answer to that is to make the AI fleets come out ahead on raw stats and numbers, so the player is both using their skills and the buffed-up Captains to win, but probably with losses (rather than like it is right now, where an optimaxed fleet can largely win for me without me doing much at all). So, to win without any losses at all, they'll have to be extremely good at solo play. That'd strike a good balance with the solo-vs-fleet crowds; solo would work, but be Nintendo Hard and take longer amounts of time IRL, whereas fleet would work more efficiently, time-wise, but wouldn't be quite as efficient, in terms of cost / benefit, game-wise.