As for bosses, it'd be ideal if every series which could have a boss (so excluding stuff like Wii Fit or Animal Crossing) had at least one.
Actually, I came up with an AC boss once: A T-Rex skeleton.
As for other bosses, I'd like to see Mumkhar, cloned Ridley (the one that appeared in the Pyrosphere is actually a clone of Ridley), the Yellow Devil, and the Dark Emperor get revamped boss fights (such as fighting both Mumkhar himself and his Metal Face mech). I'd also like to see all the bosses from the previous games return (including all Master Core forms). For new bosses, I'd like to see Andross (with three phases: His Krazoa God face (which would act like his AT incarnation), his floating head-and-hands form, and his brain form), Grima (complete with his version of Robin), Eggman and the Death Egg Robot (with a phase of him using his floating carrier or Egg Walker), King Hippo, Sigma (with his normal form and his final giant form; maybe even add in his Reaper form as his first phase), Mad Jack from DK 64, Giovanni using several Pokemon as his phases, the Titan Dweevil from Pikmin 2, the Game & Watch Octopus, a giant Nintendog and/or Nintencat (like the ones seen in the Living Room stage), one of the bosses fought in the microgame "Dungeon Dilemma), and a boss from Super Paper Mario or the Thousand-Year Door.
I'd also enjoy Hades as a boss, since he can easily make me laugh. XD