Tons of games could be in devlopment right now and could have been in devlopment for years.
Nintendo at last e3 was speculated to have new franchises but didn't show any. Various third parties have made announcements as well. Plus theres rumors.
First, although some of Miyamoto's comments were actually against such a thing there may be
a Mario game in development at EAD. Iwata asked him to make one. Hopefully, he listens.
so far lets make it into list form
First Party
Mario
Super Smash Bros 3
Metroid Prime 3(this will be big)
Pokemon Revolution
speculated
a light gun game
a survival horror fps
a strategy game(possibly Pikmin with a deeper interface. Maybe a new Fire emblem game
Second Party
Camelot RPG
Mario Party 8
Third Party
The Ea list
Ubisoft shooter
Sonic Game
Kojima Game
Thq game
Rumored Lucas Art game
Kouichi Suda game
final fantasy chronicles online
and more!