This is only a big deal imho because it's Nintendo and people love to rip on Nintendo nowadays.
If E3 is the end all be all and so important, why are both Sony and MS going to unveil their consoles before E3 begins? Also, how does not having a conference mean Nintendo would somehow get less attention? You know who actually sits and streams these boring E3 conferences? We hardcore gamers. The type of people that are going to check out what Nintendo does either way (or, for the biased people, wouldn't be interested in what Nintendo does either way).
And for everyone else who doesn't watch the conferences, you think when they log onto IGN or Kotaku or Gamespot or whatever, there won't be links to the Nintendo Direct videos, there won't be hands on videos with the games Nintendo will have, and there won't be articles about everything they did at E3? Look at how quickly LttP2 exploded. Are we honestly supposed to believe that any sort of big news Nintendo drops to distributors or the press during the hands-on sessions or to us directly via Nintendo Direct, are not going to be reported on or be as easily accessible for the lesser informed gamer than your typical conference from Sony or MS? Please.
I honestly would not be surprised if the other two companies did this in the near future. Like I said, we're already seeing it in a way with these big reveal conferences prior to E3.