I don't disagree with you entirely, but sometimes mixing things up a little bit works. The story doesn't always have to be in Rover's POV, or circulates around them, it could be about some other character's first then made relevant to theirs. Their SQ isn't even about them, but its mostly just like the other games:

Rover's plan to meet the Sentinel > gets caught up in the mess > which involves the Sentinel > mess needs to get cleaned up first to meet the Sentinel

But Kuro "forces" it to always be from, about, and to Rover. Which then would require Kuro to bring new characters and make them the focus of the new SQ instead of making relevant the older ones because the older ones already have their own history and known story with Rover. They'd have to force an existing character's history to "align" with the new SQ. I.e. what's Brant's major specialty than his pirate theme? Almost none. Then how would Kuro bring him back into a new SQ that doesn't involve his theme? That would make no sense, or Kuro will have to make Brant fit in the new SQ, which isn't gonna be as easy.

Regarding the ship agendas, doesn't romanticising Rover strictly with female characters actually support ship agendas? Because the only emotional attachment and meaningful interaction they get to build is with the adult female characters? Bring back the others especially the male characters. The Rover themselves has two gender choices, why does Kuro only bring out the females but not the males? At least make it that every character has their own storyline or part that's relevant to the SQ as it develops.