E3 just doesn't feel like the right time to reveal Mewtwo. I can't really explain it, but the way I feel is this:
E3 can go one of two ways. Either we only get about 1-3 characters revealed, or we have a reveal on the level of the Smash Direct, with 5 or more. I'm inclined to believe it's going to be 1-3, max, since there's going to be so much to discuss, as far as game modes and finer details, as well as a segment for analysis on Charizard, Greninja, Ike, and whoever appears at E3. We already have so many Pokemon revealed, and assuming there are 6 Pokemon slots, Mewtwo is a huge surprise for us. It seems fitting to make us wait until the 3DS Smash launches. If they blow their wad too early, it makes the hyp for the 3DS version peter off too quickly. No, they're going to save some blockbusters for release week.
I'm all for being pleasantly surprised, trust me. I just think that we're most likely to see a couple more veterans and a newcomer. If Snake or Pac-Man are in, they're gonna show up.
Plus, there's the tournament blowout. That's going to be the main event for a lot of people. Together with the digital event, the Q&A with Sakurai, and all the rest, it's going to be Smash Christmas no matter who gets revealed.