I feel like there's an unexamined assumption here that more flagship power unequivocally means more fun. I think past a few key skills for whatever you're doing, this isn't necessarily the case. You really want something - an edge you can leverage - since that opens up some interesting decision-making. But once you have that, adding more and more power to your flagship doesn't mean it's more fun to fly. It'll have more impact, certainly (which trades off for less impact by the rest of your fleet), but the actual moment to moment gameplay can easily be more fun when you have a little less to work with.
I mean, consider a flagship buffed to the point where it one-shots everything and takes no damage. That's not fun - beyond a few minutes, perhaps - so clearly there's a line beyond which more power is actually... less fun. The question is where that line - and its more fuzzy cousin, "more power isn't bad but isn't actually *more* fun, either" line - actually are. I think it's at a pretty low number of skills, but a lot of this is necessarily going to be personal preference. And, you have that choice!