Honestly, I hadn't considered a mission-style format akin to Conker, but that seems like an awesome idea! I can imagine playing some equivalent of capture the flag, deathmatch, and other modes that take place within modified versions of the worlds in the game, and it could have a lot of depth to it that keeps you engaged.
I'm sure other modes like the minigame mode in Banjo-Tooie would also be cool, "Mario Party"-esque additions as well. I don't see why they'd need to be mutually exclusive. I think we could have the best of both worlds.
As for how we'd play these mission-style modes, it would be cool to integrate transformations, moves you learn in the game, playable characters, and other features into how we go about accomplishing these missions. Just tons of variety in the gameplay to keep you invested would be something I would love to see in a multiplayer mode.