You aren't carving through an entire enemy fleet, ever. Think of the Star Wars movies (original trilogy). There is never a point where Luke starts snuffing out dozens of tie fighters with his one x wing. He's lucky if he can get a couple without getting too damaged to continue. It's kind of like that here.
It's really not a JRPG at all, it's more of a tactical subgame in the main game. Like the battles in total war. You can also auto-resolve said battles, as in total war, if you want to just get an average result and keep playing the grand strategy game.