but i think its a concrete possibilty that he will be in SE... i mean, unless his introduction trailer (mario attacking enemies and sonic speeding by)was just made for the updates
I was under the impression that the Subspace bomb would serve as a sort of dimensional portal allowing Snake, Sonic and possibly other 3rd party icons to meet and greet their Nintendo counterparts. This admittedly overused plot device would serve as a possible explanation for their existence. Unless all video game worlds are actually connected and devoid of such mundane concepts like Copyright Laws.

I hope that will be the case.
EDIT: Included the picture for added effect.