I disagree with you Chemical_Art. The recent changes to the Zenith and Spire Starships has made them a pinnacle of what a Starship needs to be in this game. Sure, they are damn expensive, but they are also powerful, and tough as nails. They'll last through scenarios that whole squadrons of fleetships couldn't even dream of, and they're immune to TONS of things in the process which makes that possible. I disagree with you that they're somehow less useful lategame than Fleetships. If you've ever faced an Eye on an AI Homeworld, then you KNOW why you can't bring your whole fleet to battle that. And if you only get to choose a select few ships to bring to a dreaded AI Homeworld, why not choose from the most powerful ships in the game, for their number?
If there's any complaint I have about Starships now it's simply that the recent buffs to the Zenith and Spire Starships have made all the other ones pale in comparison. Flagships seem pitiful in comparison, and Parasite Starships are extremely fragile, while Dreadnaughts are much too slow for any dedicated raiding mission (such as silencing an Eye).
In fact, if I had to choose, I would give the Siege Starships the Zenith Siege Engine treatment. They can't fire while moving, but in return they don't lag behind your entire fleet, making them impractical for most things except fleetballing and defense. Siege Starships really don't need to fire while moving anyway, and it fits their theme.
But the point is: Yes, it's true, for pure cost efficiency, Fleetships still win hands down. However, that's cost efficiency with an awful lot of assumptions, not the least of which that you can bring your entire fleet into the battle, or replace them quickly enough during a heavy engagement (that Starships may have survived and escaped); and in reality it doesn't always work out that way.