The new Zelda U should feature multiple endings.

[Super_Boom]

SvennoJ said:
Just make one awesome endings instead of a bunch of lackluster epilogues.
Different paths through the game is much better than 3 alternative endings based on a bunch of arbitrary decisions that don't affect anything until the very end.

I'd agree with this.

I love the SMT franchise, but I honestly have never played a single one more than once. I can't built up the motivation to replay the same 50 hours to get a few extra hours of changes to what I played earlier. If the entire journey was different, then that's much more appealing to me.

I think what I'd really like to see again is something to similar to Oracle of Ages/Seasons, with multiple journeys combining into one larger game. I remember really enjoying that at the time, and loving how they connected together in the end. Though I suppose considering the reaction to Fire Emblem: Fates, this probably wouldn't go over very well nowadays.