Master Chief is from the Halo franchise. However, I'm not expecting any of those 2 to be in it for the following reasons:
- They're not owned by Nintendo, not even made games for their consoles (with the exception of DBZ which made a few)
- They're a bit... Mature. Sure, the same thing happened to Snake but that's a different story.
By the way, it has been comfirmed that Captain Olimar is in the game according to this site including pictures:
http://www.craveonline.com/gaming/articles/534405-pikmin-olimar-announced-for-super-smash-bros-u#/slide/1