Ultimately, I'd like solo ships, small fleets, and large fleets to all have a place. That doesn't mean they have to be equally good at everything, though. I think we're going to need more high-level campaign mechanics/gameplay to be able to differentiate campaign playstyles effectively - right now it's more or less about combat.
One thing to note is that the only two aptitudes reasonably fleshed out with skills are combat and technology, which combine to give you a very strong flagship. Leadership is lagging very far behind, so a "large fleet" playstyle that'd be enabled by leadership + tech or leadership + (nonexistent) industry is working at a disadvantage from the get-go. Officers will enter the picture at some point, too, altering the balance of flagship-vs-allied-ship strength.
I guess what I'm trying to say is that it's too early to draw any conclusions about how these relative styles are shaping up. The stuff that's currently in place (and, perhaps more importantly, the stuff that's *not* in place) favors flagship play in a lot of ways.
(As far as a skill revamp: some of that *might* come with officers, but I wouldn't necessarily expect it. I think I'd rather hold off on it until industry and such; less chance of having to redo it again. The current skills definitely have some issues, though. Some bonuses that are too strong, major bonuses that are clumped into the span of a level gain or two, skill levels gained that don't mean much, etc. I'm looking forward to addressing all of that.)