Yoshi's Woolly World, Super Mario Maker, and Xenoblade all look magnificent, but they're kind of old news.
From this E3, my top Nintendo games are:
1) Typoman
This Wii U exclusive indie game is a bold take on the puzzle platform genre. Constructing and deconstructing words to avoid enemies and pass over hazards is a gameplay system rich with possibilties.
2) The Legend of Zelda: Tri Force Heroes
It may have soured some fans, but I'm excited to play it. Fighting baddies and exploring Hyrule with a team looks like a lot of fun.
3) Chibi-Robo! Zip Lash
A departure from the original GCN game, Chibi Robo! Zip-Lash seems more like a Mario or Yoshi platformer. No matter. With impressive level design and interesting platforming mechanics, it's definitely a game to watch.