To clarify Snake's belonging in SSBB, remember that at one point, he too was a Nintendo character. Metal Gear was an original NES which Ninty bought full license to until it got old and expired. So in a way, Nintendo still had a bit of right to put Snake in, even if Kojima begged and pleaded on his knees. :P
Sonic? He competed with Mario back in the SNES days and there was quite a huge rivalry back then which caused the two to do some awfully nasty stuff to each other.
Don't think Nintendo's gonna instantly forgive and give him instant publicity just like that. :| Besides, you think you're gonna see any Sega Reps going on their knees and beg anytime soon? Kojima's just plain weird, the rest actually have business sense. :P
I'm so gonna get pwned aren't I?