In an interview with JeuxVideo Magazine, Michel Ancel (creator of Rayman and the original Beyond Good & Evil) is quoted as saying that Beyond Good & Evil 2 is in preproduction and has been for about a year or so:
According the rest of the article, about a dozen people are working on the project. Ancel wants to maintain continuity with the first game, and dropped some hints as to what that might imply: "Large variety of stages of play, lots of emotion in the gameplay, characters you can get attached to. This time, we're addressing the fate of the planet." He also mentioned that animals will play a role in the game, although there's very little elaboration on that point.
Considered one of the best games of 2003, the original Beyond Good & Evil was critically acclaimed but commercially panned. As someone who has very little faith in the creative capacities of the giant publishers in the industry, I'm glad that Ancel and his team are working on a new game. I can only hope that Ubisoft gives it the green light. Perhaps we'll get an official announcement at UbiDays -- coming on the heels of another BGE2 rumor, I think that's likely.
For any readers in France, the full interview is in JeuxVideo Magazine, no. 91.