Nintendo May Not Have Direct for E3 2016
Might Only Be "Legend of Zelda"
Nintendo announced that they will be having a large Nintendo Treehouse presentation for just "The Legend of Zelda" for the Wii U/NX (though only the Wii U version will be shown off), where that will take place around the time Nintendo would have their Nintendo Direct presentation- 9am PST/12pm EST.
With the announcement of the Nintendo Treehouse presentation and no word of a Nintendo Direct, it looks like Nintendo isn't going to have a Direct for E3 2016 and "The Legend of Zelda" will be the only game shown off. Nintendo may not reveal any new games coming out in the future, though that isn't clear as of now.
There is a contest where you can get the chance to go to E3 and play "The Legend of Zelda" for the Wii U, as seen on the Nintendo E3 page. The contest goes until May 10.
Source: Nintendo E3