OoT has some of my favourite bosses ever: Phantom Ganon, Volvagia & Twinrova. Simply because of the awesomeness of these three, OoT wins for me. And the rest of them are pretty fun too.

Not to say MM bosses aren't good, but really I only like Goht. Odolwa is a good fight, but he's too annoying. I just hate Gyorg, and Twinmold doesn't do anything, they just fly around and wait to be killed.

Final bosses... I don't really know. I like both final fights. Maybe MM's is better, it changes more. Incarnation always makes me laugh, and then there's Oni-Link... <3

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Two things:
1) Zora -> Rito = true
2) It's Soul Calibur, not caliber.