Well the thing is, I would think Microsoft would want a character they had a hand in creating as part of their brand identity. Yes, they own Banjo, but they know that they only acquired him from Nintendo after the fact. I think he should've been added back in Melee. Perhaps the reason they were so eager to let Banjo in is because they felt the same way. He is, for all intents and purposes, a Nintendo character, as he debuted on their system and was published by them.
Chief, though, he is pure Microsoft. It'd be kind of unprecedented for them to have the mascot of a competitor in their game, and would serve as a new gap being bridged. Possibly even open the door to Sony mascots if they were willing to play ball?
And again I say unto you, no car gets in before Nintendo's own vroomy lad. I've actually been busy drawing up a moveset for him.