So then why didn't Sakurai care that he was advertising Metal Gear with Snake? Simply because they're friends? If enough people vote Banjo, I'm sure Sakurai can look past Microsoft currently owning Banjo and recognize that he used to be a Nintendo icon. He was the byproduct and symbol of one of Nintendo's greatest line of second party games. He's had 4 Nintendo games and only 1 MS title. He CERTAINLY makes much more sense than Snake ever did, and the poll didn't claim to only accept Nintendo-owned characters.
Furthermore, Banjo was already confirmed to have been considered for Smash Bros on the N64. It really isn't all that big of a stretch.