When you think about it E3 conference as a hardware maker is supposed to the overall breadth of the hardware platform. So things like third party "megatons!" and showing off third party software is as much a part of these Sony/Nintendo/MS conferences as the 1st/2nd party games themselves. That's part of the whole point of having the "big stage".
But third parties aren't supporting Nintendo or giving them any exclusives. Even Ubi Soft screwed Nintendo with Rayman. And the year before of course we got that EA "unprecidented support" speech, which went nowhere.
So I wonder if (privately) Nintendo's reasoning here isn't "why should we spend a ton of money on a big E3 event when it's really just going to be our games on stage? If we're just showing our games to our fanbase, we can do that much more cheaply with Nintendo Direct".
I think that has something to do with it.
The third party community has largely abandoned Nintendo and maybe throws them a few token ports at best, and even those I'm sure Nintendo is looking at the sales and realizing multi-plats are not helping the Wii U at all. The two big third party IP that Nintendo does have -- Dragon Quest and Monster Hunter are handheld centric and mostly only relevant in Japan, so again the E3 show in America doesn't make sense for those either.
Maybe this is more of an admission from Nintendo that they basically have to do all the work in selling Wii U/3DS in the West, and they can effectively market their Mario/Zelda/DK/Pokemon/etc. games directly to their fanbase with Nintendo Direct ... it's like why bother spending a ton of money on a big Christmas dinner when it's only been your immediate family showing up the last 4-5 years.