One website is reporting that Beyond Good And Evil 2 will not be a direct sequel to the first installment of the game. Let's Play Video Games says they have a source that's "familiar" with the negotiation process between Ubisoft and Michel Ancel and says neither party is referring to the game as "Beyond Good And Evil 2". Instead, the game is to be a standalone reboot with portions of the first story being told within the new story. Here's a snippet from the article that's relevant...

According to our source, the currently planned direction for the game is that it will partially retell Jade’s origin tale from Beyond Good & Evil, flesh out Peyj’s backstory, then continue to extrapolate on the ending of the original game. 

That certainly would make sense as Beyond Good And Evil didn't exactly have a booming fan base, but I'm not too familiar with the site or their unnamed source so it could really just be an educated guess. 

I don't imagine too many people being up in arms if that is the case. I think what's more important is making sure you bring back the classic gameplay people loved and tell a good story. I hear more people talking about the gameplay and concept than I ever heard people talking about Jade. 

So while I don't believe it until someone more official confirms it, I could certainly see that being the case judging by the one image of the game we've seen so far...which doesn't feature Jade.