Alright let me jump on the bandwagon.
In addition to all that has been said I predict an Animal Crossing game for Wii U and an Amiibo focused game for both Wii U and 3DS.
As of Microsoft/Rare, I think they will unveil a Battletoads game as a downloadble only game, and... perhaps Banjo-Threeie?
Regarding Playtonic I predict a playable demo of Yooka-Laylee of the stage we have seen before in the trailer / kickstarter video. (Not sure if they will attend E3, but one can dream right