I never said anything about Kefka. I've never played FF6 so I can't comment on him, but from what I've heard nothing but good things about him as a villian. I disagree about FF7 though, Sephiroth might not have been the main point of the story, but neither were only Cloud, Aeris and Tifa. The main point was the main character party saving the world from SHINRA, and then later on Sephiroth. The whole thing with Cloud and Zach and Aeris and Tifa was just part of that, and honestly not that interesting and just unnecessarily confusing. But as far as villians go, the whole "insane villian" is lazy IMO, and if someone's gonna do it then they need to put a LOT of effort into making it interesting, and JRPG's rarely go out of their way to make an interesting character when a cliche will do.
As for looking past the "save the world thing", it's kinda hard when it's the main point of the game. If I have to look past the whole point of a game to have fun with it, then it's a bad game and a bad story. It's like saying "Star Wars is great if you ignore all the stuff about the Empire".