Starsector is a single player game. Player centered. Not AI. I suspect that a mess what happened in the current release is at least partially is a result of paying too much attention to AIvsAI scenarios.
I would disagree here. AI vs AI is important from a balance perspective. While it's true that the player is going to have the most impact and probably
should have the most impact, to say that you shouldn't pay attention to AI ships because it is a single player game is a recipe for disaster.
98% of the ships on the field are AI ships. There is certainly a point where "the player does everything" turns from fun into tedium imo. The player should be the driving force, but AI allies should have a definitive use and for that to happen there has to be balance considerations around AI vs AI.
As far as the OP, I can't really say I have much of an opinion other than I don't think all ships need to be player pilotable - though that doesn't mean I think the Guardian should necessarily be excluded for that reason alone. I'm pretty indifferent really.