That said, it seems like some nerfs to the mkI starships to compensate for the knowledge-free aspect wouldn't be out of order, and would help the mkI fleet-ships compare better against them.
I'm not in favor of this at all, as then it's not representative of the other higher-mark starships. A single mark I starship should be worth quite a lot of fleet ships, perhaps the entire cap of a single other fleet ship type, but at the same time they shouldn't be able to work on their own.
Basically, the question of "which is preferred" should ultimately be irrelevant. The AI should be tough enough on its planets that you have no hope if you don't build all the starships plus all the fleet ships you can. Trying to choose one or the other should be like trying to choose infantry or cavalry in terrestrial RTS games: in some cases you can get away with it, but when you can you're not really being challenged to your fullest so it's not exactly a true test of it.
On the other hand, it's not necessary that everything be equally useful, since the player is presented with several strong motivations to "do both", so to speak. Currently things are skewed towards being able to "just do starships", and that needs attention.
I'm honestly not sure that it's "just do starships" except in a few cases, such as things for taking down heavy defenses (forcefields, etc). In those cases, at the moment the siege starships and bomber starships definitely outstrip their smaller bomber counterparts. And you know what? I think I'm okay with that, for the moment. In a perfect world you'd need both, but the bomber/siege ships feel cool and seem better than managing hundreds of smaller bombers. Not that I want to keep it that way forever, but I don't think of it as an egregious wrong situation that we have to leap on to correct immediately.
We'll have to see how it all shakes out, I know the balance is not perfect or even close right now, but starships should feel... big. When they don't feel big, they might as well just be a few fleet ships. Possibly starships are simply way too cheap or something along those lines -- perhaps they need to be 5x or more expensive across the board, so that the fleet ships are more attractive for cost reasons. That would also make starships take 5x longer to produce, as the burn rate of starship constructors is the constant.
I guess that's basically what lanstro and others were saying, in the end. And... yeah, I can see that. I think I'll try something along those lines. In combat, starships feel about right to me, but their cost-to-benefit ratio at production time might be out of whack, and I haven't been focused on that part as much.