The confirmation came in the latest Devs Play video from Double Fine, where Tim Schafer played an hour of the original Beyond Good & Evil alongside the game’s producer, Michel Ancel.
At the end of the video, Schafer directly asked about a sequel and Ancel’s mentality. The question kicks in at 1:07:49, for reference.
“You’re still in the headspace of this game because you’re making a sequel right,” Tim Schafer asked. “You’re thinking about [the Beyond Good & Evil] world still.”
“Yeah, but it’s difficult because it’s hard for me to redo the same game two times. I don’t know how you’re going to manage that for Psychonauts 2,” Ancel replied.
I hope so - I'm about to finish up Beyond good and evil HD on PS3/PSN :D