On one hand, the fact that half of the characters appeared in the game with the Villager being previously dismissed as impossible by Sakurai himself and no one predicting Wii Fit Trainer makes the leak seem legit. It's a valid possibility.
On the other hand lies the other half of the characters, Little Mac, Pac-Man and Mii, who weren't shown, partially contradicting. Well, whether this debunks the leak or not is quite hard to determine.
To elaborate: the leak said that, at E3 2013, the six characters, Villager, Mega Man, Wii Fit Trainer, Little Mac, Pac-Man and Mii would be shown. What happened is that only the first three characters were. Does this make the leak instantly fake? Well...
If you assume the source got this information from when the development staff was planning what would be revealed on E3, there's always the possibility of team deciding of just showing the first three characters, saving the latter three for other occasions, like Little Mac.
Assuming this is fake and just a lucky guess, consider it damn lucky. First, there's the fact Sakurai had said that characters from Animal Crossing were unfit for the series. As such, no one expected the Villager showing up. Many people vouched for an AC character, no doubt, but the expectations were low. As for the Wii Fit Trainer, well, even Sakurai himself stated no one would guess her.
While the possibility of this leak being a guess exists, it seems hard to believe given the circumstances I just mentioned.
However, there's another possibility few people seem to consider: the leak is partially true, partially false. The inside information was just about the first three, but whoever leaked it decided to add three more characters to create confusion. The credibility of the leak would be damage and the leaker could get away with the same argument people use to defend it as false: the fact not all characters were shown. Hell, the leaker could even be trolling!
Fast forward to April 2014 and the same leaker reveals another bunch of information: on the Nintendo Direct, the following characters would be revealed: Shulk, Palutena, Chrom, Chorus Men and a Pokémon from X/Y. Of these five, only the last one was true, with Greninja being the revealed choice.
Pretty similar situation as above. Could be true, but the source got information from a different stage of planning and things eventually differed, it could be another lucky guess or it's once again partially true, partially false, which in this case seems an hard to believe hypothesis, but definitely not impossible. Nothing stops a leaker from distorting facts, after all. (Hell, I could say many journalists nowadays do this, but that's irrelevant to the subject at hand.)
What I mean to say is there are many ways to interpret this situation, which leads to different conclusions on whether the leak is true or false. I'm a bit skeptical about all this, although I think it's too much of a coincidence the leak mentioning both Villager and Wii Fit Trainer, characters that no one thought they would be in, yet they were revealed. It adds to the legitimacy of the leak, much like how the absence of the other character hurts it.
One last thing I want to say is how I believe there will be no way to fully determine the legitimacy of the leak. Even if a character is disconfirmed, there's the possibility of information having been added to the true information. Even if all characters are confirmed, there's the inconsistency of the reveal circumstances.
All in all, it's a matter of time. If the last outlandish character, the Chrous Men, is revealed, that will add a lot to the leak's credibility, notably, the first hypothesis I mentioned above (actually true information, but changes of plans before the reveals).
(Whew, this took a while...)