Personally, I think it is a good move for them. The presentation would be mostly about games for the Wii U since they have been showing off the 3DS big time lately, no one but the investors and analysts in the audience care about the sales numbers or marketing schemes, the press in the audience care about the games. Instead of trying to cram everything into an hour long presentation which never works, they are having several closed door events for the press/investors/distributors/etc for a more intimate look at the company and the games.
Meanwhile, I could very well see them broadcasting their direct at their booths in the morning before any booths open, and then allowing people to play the games they just showed immediately. The public that is there gets to hear the announcements first hand, and then gets to put their hands on the games right then and there. They are bypassing the droll parts of E3 while still giving the people that are interested at that stuff the attention they want, in a better space. A smaller class size is always better.
Iwata mentioned that they would be "continuing to investigate ways to deliver information about our games directly to our home audience around the time of E3." Obviously they will have Nintendo Directs....so why not just say that? It could mean that they are looking into providing game demos to download on the eShop after the Direct announces them, giving the home audience the E3 experience. The games they will be focusing on will be releasing by the time this fiscal year is over, so the demos should be solid enough to release. I'll admit that is some very wishful thinking, but it would be an incredible move by Nintendo.
E3 has become increasingly irrelevant over the years too. The conference itself hasn't puled in as much money as it has in the past and isn't nearly the big showcase it used to be in the late 90's/early 00's. Apple is having their WWDC thing the very same week, which will definitely steal away some of the E3 attendants. Sure it's a little bit of a bummer that there won't be a press conference with the big stage and everything, but it also means that we will get what we have always wanted out of E3. Games, games and more games.







