Ubisoft's good and growing relationship with Nintendo could definitely lead to them getting a character in the next Smash game. Namco's been in a good relations with Nintendo as well, and their work on the previous game may have contributed (but not been the only or even necessarily strongest reason) to Pac-man's inclusion in the game, so maybe something similar has happened with Ubisoft. It provides a perfect opportunity for the discussion and legal negotiations to be done, as well.
That said, there's nothing we can be sure of yet. The two companies being on good terms could certainly lead to this happening, but it's far from being a guarantee. Star Fox's guest appearance on it's own doesn't mean anything at all for Smash, either.