A couple months ago before the Nintendo Switch was revealed and released, Laura Kate Dale reported that Beyond Good And Evil 2 will be a timed exclusive for the Nintendo Switch and that it’d be at the Switch presentation and it was not at all. There was a slight hope for it being at E3, but it may have been shot down for another event after E3.
Creator Michel Ancel revealed that the game will not be making an appearance at E3 in a reply on Instagram. The fan specifically questioned on whether we would get Beyond Good & Evil 2 footage, concept art, music or anything else, to which Ancel replied:

“Mhhh, not sure that E3 would be the best place to showcase Beyond Good & Evil 2 but we’re working on the game so sometime this year, you should hear about it!”

We will have to see where Ubisoft and Nintendo will reveal news on the title.