Thanks for the suggestions !
I thought about that a bit, and I think the best option is still to come up with RTS-like controls, but for only one ship and with much more complex commands. Like you’d have pausable tactical view, just like in Homeworld. You’d assume the role of a commander, set courses (perhaps with a delta-v system to make it more interesting), designate targets, coordinate the strike craft/smaller ships carried by your capital ship, decide when to use special abilities, coordinate weapons and that kind of stuff. Outside of combat you could take direct control of smaller crafts to perform exploration/salvaging tasks, and you could even have overwatch missions where your big capital ship provides support to ground forces or personel, that would confront you to ethical and story choices (like do I let my marines getting killed or do I blow up this city with my massive dreadnought cannons because, as I have angered the local weapons consortium, I can’t equip surgical strike missiles).
Outside of that, you’d be able to walk inside your ship in third person, talk to people, see its systems, move the narrative forward mass-effect style. If the ship is sufficiently massive, it could act as the game’s main hub ; I could totally see a BSG-like story, where you have to go from point A to point B through carrying refugees in the middle of a war, and every new people/personel that goes on board unlocks the possibility for new combat abilities, systems and story options.