They're both worth it since it's an awesome game.
But I'd make sure to play the SNES version at least until the episode when you save Celes, otherwise you get deprived of a great scene.
Actually, I believe the Celes beating scene is in the GBA ROM as well and could be unlocked via some debugging or ROM hacking, but I have no proof to demonstrate this at the moment (though I have my very good reasons to think so).