Sakurai/Sora/Bamco had access to all of GameFreaks' (and Nintendo's/Capcom's/Sega's for that matter) resources long before development even went underway. Though it seems unlikely any "focus group" type deal happened, I wouldn't rule it out. Truthfully though, I just feel like Sakurai looked at what each character was capable of, would be "cool" (which wouldn't be too far of a stretch to presume would be seen as "cool" by the fanbase, which speculated/intended or not, could lead to some very easily predictable "popularity").
As far as this pertains to the leak, "Pokemon from X/Y" seems to be a special case this time around, as the games/Gen VI didn't release too long ago. It's neither a stretch nor presumptuous to say that it was an easy/generally broad guess that left little room for error, far more so than the case for previous Smash games (Melee came out less than 2 years after Gen II's debut, while Brawl came out 2+ years after Gen IV (even longer than that considering the Gen IV rep in the form of Lucario was shown even earlier than that), but at the same time it seemed like a fairly decent chance that there would in fact be no Gen VI-specific-debut (as in no Megas, "promoted" Pokemon, etc.) newcomers on the roster. All in all the thing that bugs me the most, thereby keeping my skepticism intact, is that this information came the day of the Direct. Had "Pokemon from X/Y" been included with the original "Mega Man/WFT/Villager" prediction, there would probably be no doubt in my mind about its legitimacy.
On another note, I feel like this "drama" between the "leakers" getting fired/leaving the development team or whatever is nothing more than glorified romanticism on our part. It more than likely is as simple as "guy gets a glimpse of leak-worthy info, passes it off to friend since they know they can get in trouble for it, friend decides to get 15 minutes of fame for information that may or may not be true (either because things were subject to change, or because someone was bored enough to fabricate things to make it "more interesting"), Smash fanbase goes rabid and writes these walls of text debating what the true scoop is."
Well now I've said far more than I intended to upon coming in here. So I guess the leaker succeeded regardless of intent.