They said they were working on other things outside of the Metroid franchise nearly 2 years ago.. Don't act surprised.. Also Reggie said they were hard at work and we'll be blown away with what they have in store, not to mention we've heard rumours of them developing more than one title which would meant it'd take longer for the games to be made and also they WERE working on a Zelda project which has since been canned which would also have taken dev time.
Perhaps that Zelda was the other title they were working on? Either way, E3 2010 will hold the answer for sure!