It's been confirmed that Retro Studio's secret project was the new Donkey Kong Country: Tropical Freeze, but they almost went with another Metroid game. I guess we'll have to look beyond Retro Studios for some Star Fox love.
Super Smash Bros., for both 3DS and Wii U was shown, and Fox makes his expected appearance, but no other Star Fox characters were seen. Keep an eye on the official game site for new character reveals. There have already been two today: Animal Crossing's Villager and the Female Wii Fit Trainer.
Other than that, Nintendo had a great press conference, in my opinion. They showed lots of good looking, interesting games and provided a couple of nice surprises like the sequel to Xenoblade. The only thing that could have made this presentation perfect would be a surprise Star Fox (obviously) or actual footage of the new 3D Zelda game they're apparently working on (NOT the Wind Waker remake, which also looks fantastic).