I can only speak from my perception. Along with all the other issues not even bothering with a conference (which I usually watch all 3 of them) just sends me a signal of "we don't care" or they "don't have anything to show".
Then again, I'm probably not their target as they have almost completely lost me as a customer (still love my 3DS).
The conference is where the big announcements come from. Now I'll probably just read a twitter feed or some random thread on GAF about things instead of knowing when/where I could have seen it LIVE.
I get why already entrenched fans don't care much, but for somebody that is mildly interested in Nintendo at this point, a conference with some actual thought and announcements goes a long way.
EDIT: I understand it's "just the conference" they are skipping. But it seems like a shitty way to go about things. Every company is going to have youtube videos, developer interviews ... and most people will look for what they want to see. The E3 presentation is for people that are interested enough to watch without having a 'direct game' or 'interest'. It's a big presentation that you'll only see once a year. And they are skipping that so they can show me Mario Kart videos on youtube.
THEY ARE NOT SKIPPING THE CONFERENCE.
Is is just not live, that is all. It is prerecorded. I have a question, are you going to e3?