Don't worry, Nintendo hasn't forgotten about Metroid
Sadly, the Metroid franchise didn't show up in any capacity at E3 this year. No, I'm not counting Super Smash Bros.
Don't worry though, because Nintendo hasn't forgotten about the franchise. Don't believe me? Then take Shigeru Miyamoto's word for it.
Kotaku's Stephen Totilo flat out asked Miyamoto about the future of the Metroid franchise during E3. Miyamoto deferred to Shinya Takahashi, director of the Metroid Prime games. Takahashi recognized that it's been a while since we've seen a Metroid game, but sttated that there have discussed the future of the franchise internally, but aren't really that close to showing anything off just yet.
As for whether or not it would be a 2D side scroller or a 3D first person affair, Nintendo isn't ruling either out. In a perfect world, we'd get both.
Let's hope we get both.