More from NeoGaf:
Nintendo pulled trailers of Retro's new game,EAD Toykto's new game & demo of Aliens.
Edit: COD:BO2 is still development, Retro sounds like a mystery because it's in "showable" form and could be shown soon (though not necessarily at E3). EAD game was in pre-alpha stages so they just felt it wasn't ready yet. Nintendo didn't want to show games that weren't in the launch window.
It does give reason for the odd 3DS games discussion and long draw out on NintendoLand.