He just confirmed it on Geoff's stream.
Edit: found another source.
http://nintendoeverything.com/ubisoft-says-beyond-good-evil-2-is-still-happening/
Edit: found another source.
Beyond Good & Evil 2 was first made known nearly a decade ago. Yet despite that, we’ve heard next to nothing about the project since then.
Ubisoft CEO Yves Guillemot did offer up some words of encouragement during the official YouTube E3 stream. He told Geoff Keighley that Beyond Good & Evil 2 is still on the way.
http://nintendoeverything.com/ubisoft-says-beyond-good-evil-2-is-still-happening/