Companies have changed their E3 plans last minute in the past. There were even a lot of rumors last year that Nintendo pulled the plug on Retro's reveal -- what we now know to be Tropical Freeze -- at Retro's behest.
Rumors aren't fact, though. If they are just rumors, there is no proof that Nintendo really did pull Retro's game, no? I wasn't following that at the time, so if there was concrete or near-concrete proof, pardon my ignorance.
Things can and do happen. When you couple that with the fact that Nintendo''s presence at E3 was anything but traditional, and that newcomer reveals are being packaged much like MvC3 like we saw with Wii Fit Trainer hours after the Nintendo Direct, it isn't that far a stretch to think Sakurai could of held back on some reveals for the sake of spacing things out or just focusing on the three newcomers shown.
Consider for a moment the amount of work that would have gone into preparing reveals for another 3 characters. You'd need to reveal some more stages, you'd need good-length cinematic and gameplay trailers for Little Mac and Mii, and a Mega Man length one for Pac-Man as befits his prestigious status as a gaming icon. They
could have decided to drop all three characters at the last minute, but that's one hell of a drop-fully half of their E3 reveals for the centerpiece to their presentation!
And this source sent his information only a week before E3, correct? That's not much time, even assuming a lag time of a couple weeks before.
The Smash presentation we got doesn't feel like half of an E3 presentation that was cut at the last minute. It feels like a complete presentation, at least to me.
Plus, the idea that they would drop both of their huge third-party newcomers at E3 feels odd to me.
For my money, the likeliest explanation is that the source got carried away or was misinformed and assumed that certain characters on the roster would be shown at E3. Could still be a lucky guess as well, but that's significantly less likely.