YouTube - ‪Zelda Overture - E3 2011: Nintendo Conference‬‏

because it doesnt take place in hyrule

LOL I also noticed that, was kinda miffed about it tbh x_x

When i noticed that i started to think in a possible Majora's Mask remake on 3DS.

There's always hope, They really only showed the mainstream games though Didn't see any of the DS/gameboy titles up on it Should of showed ALL the Zelda games (god forbid CDI versions)

Same reason they don't have the Gameboy Color titles or the DS games up there.
It's a side story.

It was strange seeing how MM was in the first Skyward Sword trailer.

this .

Added after 2 minutes:

MM is the direct sequel to OoT, that's why it was in the first SS trailer.

And Links Awakening was the direct sequel to Link to the Past. Phantom Hourglass was the direct sequel to Wind Waker. Those wasn't there either.
Notice that all of the games in the overture were based in Hyrule. No four swords trilogy, no oracles, no DS sub-series, etc.

The first trailer was specifically the 3D Zelda games up until that point. This one recapped all of the main games in the franchise.