So, I delved a bit of deep thinking with all the evidence we have gathered here so far, and I think I have a simple explanation regarding the gematsu leak, and whether or not it can be seen as credible.
First off is the first leak, where he said that "Animal Crossing Guy," Mega Man, Wii Fit Trainer, Little Mac, Pac-Man, and the Miis were all going to be shown at E3 2013 as playable characters. The second leak had Shulk, Palutena, Chrom, Chorus Men, and "Pokémon from X & Y." In between, we also got Rosalina & Luma, a character he did not predict. We now know that all six characters in the first leak are playable, two from the second are as well, one has been disconfirmed, and the other two is still at large. We have since learned that he is affiliated with Namco Bandai (given that he called them Bandai Namco, he's possibly a foreign branch), and that Shulk is most definitely in the game, implying that he may have been finished a while ago, and he got to see him in action. Beyond all that, it's likely that his information is dated and his fourth tip was simply an assumption rather than a real leak as he didn't divulge any further details. It's also worth noting too that leaks that are disconfirmed generally just fade away, with the leaker often just giving up and going home. However, the gematsu leaker is still going at it, and will likely return at least twice more before launch.
So, let's look at the evidence. He may have known from the very beginning that these twelve characters were at the very least, had spots reserved with other slots for potential newcomers still open for consideration. The first six characters may have been leaked specifically because they were all considered for a reveal at E3. However, they decided to only settle for Villager, Mega Man, and Wii Fit Trainer. Mega Man alone would have generated enough hype without drowning out Villager and WFT. Villager was likely a guarantee because of the very first trailer essentially serving as an introduction for the initial ten. But WFT was shown on the floor at E3 simply due to the fact that a character like her couldn't generate hype on her own. As a result, Little Mac, Pac-Man, and the Miis were pushed back in order to not distract from the newcomer reveals shown up to that point. The latter in particular was most likely not even finished yet given the lack of a specific name, and if I had to guess, the Miis originally only had the Brawler class, and that Swordfighter and Gunner were implemented a little while later.
Next comes Rosalina, and this one is simple; up to her reveal, none of the other Nintendo Directs were showcasing any newcomers, which was why he didn't leak the second list until shortly before Smash Direct, in which she and Little Mac were revealed.
Next comes the second leak, where he said that Pac-Man and Miis were still on their way. Chances were highly likely at that point that we'd get reveals for them at E3 2014, and that he had yet to know the Mii's final name. In addition, he also predicted Shulk, Palutena, Chrom, Chorus Men, and "Pokémon from X & Y." We got Greninja, and he reiterated in the third leak that Mii Fighters, Goddess Palutena, Pac-Man, Shulk, Chrom, and Chorus Men were all going to be playable, but also added that either Lucas or Ness--the former more likely--were to be cut, and that there'd be character DLC plans, and thinks Nintendo's just being greedy. Since then, we got Mii Fighters, Palutena, and Pac-Man, but Chrom was disconfirmed. Worse yet, the night before Chrom's disconfirmation, he told us to enjoy Shulk. The next morning, he let slip that he at least had affiliations with Bandai Namco when saying that Nintendo keeps character details secret, and that Sakurai can change his mind at any moment. But, he reassured us that Shulk is in the game, guaranteed.
Now that I filled you up on all the details, it is likely that "Animal Crossing Guy" was a placeholder name similar to "Pokémon from X & Y" except it was until they were to settle for Villager as a name, while Greninja was simply selected after looking through concept art. Chrom is a bit of a similar case, except you can look at it closely towards Villager's scenario in which a slot was indeed originally reserved for him since Smash 4 began development shortly before Fire Emblem: Awakening came out, and Chrom looked to be the next main protagonist. The quick and easy guess as to why Chrom was cut was because he wasn't really the main character of the game but Robin, who had a much more unique moveset that would have been new for Fire Emblem, so Chrom was scrapped in favor of Robin.
Where Lucina fits in makes perfect sense; she was originally going to be an alternate skin for Marth (thus looking strikingly similar to him and having the same moveset), but due to the minor differences in size, was restructured as her own character. This essentially means that Marth will not have an alternate skin at all, and most likely, neither will Lucina (though apparently, she can put on and take off her mask using a taunt, making that a pseudo-alternate skin, but not really). This could possibly lend itself to the reveal of more clone characters originally planned to be alternate skins or color swaps like Dark Pit or Impa (assuming that it's her and not Ghirahim); there are, after all, hints and teases of these two being playable. Either way, this essentially confirms that he doesn't know the full roster (it'd make sense that the characters he doesn't know about will most likely won't be revealed until after launch with maybe one or two exceptions).
Where the Ness vs. Lucas bit came from remains to be seen, but it is unlikely to have been tied to Lucina's inclusion if it turned out to be a really late addition. We may never really know if there was indeed a dispute between the two unless Lucas is indeed cut from the roster. I initially debuffed the leak altogether due to the character DLC contradicting what Sakurai had said before speculating on the possibility of this DLC being the amiibos; if his information really is dated, after all, then he probably assumed their NFC plans were for DLC instead of the figurines that we are about to get. However, hints and teases coming from Captain Toad "wishing he could join the fight...someday" as well as the Rayman trophy suggests that maybe we will indeed get character DLC and that those two could be it. It wouldn't be outside of Sakurai's capabilities to alter Rayman's 3D model a bit and make him into a playable character, but if his inclusion turned out to be very late, Rayman could be reserved for character DLC at a later date.
The naming of the Chorus Men and Bandai Namco may suggest that he may be a Namco employee in Tokyo, but knows how to coherently type in English. This is due to the fact that in the states, the Chorus Men are called Chorus Kids, and Namco Bandai is what we call the company there as well. But if he is employed over there, it leaves one to question what position he is working in in order to get the information that he had, can guarantee that Shulk is playable, and yet still not know everything and get a wrong choice. He can't be a developer or programmer since he'd known of the switch. He isn't a tester either or else he would have spilled the beans on the entire roster. And I doubt he'd be working at archives or mail room since he'd probably would not have such heavily dated information, nor known about the Ness vs. Lucas debate. He might be in marketing, but there's no way to tell what Namco's marketing branch is in charge of regarding Smash Brothers until after launch.
Of course, none of this will matter at all unless Shulk gets confirmed. Chorus Kids as well, I guess, but for all we know, they may have been planned as a 3-in-1 character but replaced with another Rhythm Heaven character due to complications with the 3DS hardware (thus explaining why Ice Climbers haven't been confirmed yet); besides, we know we're getting a Rhythm Heaven character because of the Sneaky Spirit enemies. This pretty much means that against all odds (since he has confirmed that he doesn't know for certain the entire roster, nor knows of any other newcomers that will be in the game), the gematsu leak's one last shot at redemption is Shulk. He has guaranteed us that Shulk will be playable. That pretty much means that regardless of whether or not the Chorus Kids are playable, if Shulk isn't playable, then we will know beyond a shadow of a doubt that the leak is fake.
Judgment day for the gematsu leak is soon upon us.
EDIT: Wasn't made privy of any warning. Sorry.