I don't know what it is with the Golden Sun suggestions but those games pretty much embody almost every dealbreaker prophet posted in the OP. The exposition is like an hour of talking, they literally don't spare a single jrpg/anime cliche, and the characters are bland as hell to boot.
I'll suggest Live-a-live, which is a semi-obscure Square RPG for SNES that was never released outside of Japan (but has fan-translations available). Game is split into a number of chapters which can be completed in any order, each in a different setting, and each with differing characters and gameplay elements. Completing them all unlocks a final chapter that ties all the previous ones together in a pretty spectacular fashion. Great soundtrack by Yoko Shimomura as well.