The game should be good without mods. If I pay money for a game, I want a game, not a game engine that needs third party support to polish it up. I should not need to rely on mods to have a good game. If I need to mod a commercial game to have a good game, I rather play make-believe and say "I WIN! GAME OVER!" and look for a better game that does not need mods (or a free game where community support and development from anyone with the dedication is the point).
Respec during the game means I do not need (to make or download) a third-party tool to cheat that feature in for me.
If you playing in vanilla and you are not playing the carrier specialist, you usually fly capital ships. There isn't much choice in the capital ships you can fly either.
I fly the paragon for like 99% of some of my games. I don't complain. I love that ship.
Before mid to late-game, capitals are usually not an option. I need to make do with whatever ships as I acquire them, and warships are much more common than carriers. Even late after I get the capitals I want, I still occasionally use smaller ships when they are more useful, and the skills are still useful for them. With carriers, player has what? Drover, Heron, Mora, and Astral?
And yes, Paragon is nice. It is my flagship of choice, although I do not always fly it. In my current game, it was almost the very last ship type I acquired (I had to raid Culann with a pure phase fleet to get the blueprint). I had to make do with other ships until then.