i prefer patapon because it has a story, it's cuter, and it has more depth than rhythm heaven with equipment, classes, leveling, etc.
patapon is more of an rpg-rhythm game, and rhythm heaven is more of a microgame rhythm game.
they're both pretty good though.
I've never played Patapon before. But I watched some trailers and I like Rhythm Heaven more. Mainly because it are mini-games, and it has a larger variety of games and styles. I just think Rhythm Heaven is more diverse.
Both games are rather different. Patapon has an RPG element in it, and the rhythm factor isn't really the main thing in Patapon (you just learn some commands and you're basically just repeating them over and over) compared to Rhythm Heaven. Rhythm Heaven is more of a mini-game style with the mini-games focusing on the rhythm most.
But both are excellent games though, can't really decide which to pick. :3