If the Wii U was getting tons of third party support and Nintendo had some exciting announcements to make on that front, I think for sure they would opt to have a big stage this year.
But that's not the case and largely it's just probably going to be the usual Nintendo games (which will be great of course) and the two Platinum Games most likely, so yeah I kinda get their reasoning.
Mario 3D/Mario Kart/Wind Waker Reborn/Smash Bros/Pokemon primarily appeal to Nintendo fans, and that can be communicated to them through a Nintendo Direct.
Even the whole blue ocean/casual crowd, where it made sense to have a big E3 show to show off to CNN/Time Magazine/etc. and get the word out there about Nintendogs or Wii Fit or whatever ... it doesn't make sense anymore because that audience has largely moved on too, so no point in renting our the big stage. It's probably a good thing anyway that they not spend 20 minutes on Wii Fit or some new casual fad (though it seems to be like Nintendo has stopped chasing this dragon anyway and is just content with making sequels to the Wii/Mii titles and seeing if they still have some life).
