The 2006 Brawl poll was Japan-exclusive and by then, Metroid was niche there and Punch-Out!!, never that big in Japan from my recollection, was on a hiatus so Ridley and Little Mac likely would have done poorly. I also recall Wolf being a lot more highly requested in Japan than Krystal so I doubt that would have made a difference for Krystal even if Wolf had returned. As for Villager, while an Animal Crossing character probably scored high, I doubt popularity was what got Villager in this game but instead Sakurai having a change of heart. I will give you Isaac thought; he likely scored very high up there.
The reason why I say Mega Man is the only one is because Mega Man was the highest third-party after Sonic according to Sakurai. Given that most, if not everyone feasible, likely got in Brawl's roster already, I also feel as Mega Man may have been the highest character in the Brawl poll (even above Isaac arguably) that could have become a newcomer for this game (and he did). As for everyone else... Sakurai has never commented on anyone else being added due to fan demand on the initial roster, just Mega Man. Plus I don't feel as any Nintendo characters that did get in (even Little Mac) were on the same level as the massive pre-Brawl fan bases we saw (as well as what Mewtwo, Mega Man, K. Rool, and Ridley commanded for pre-Smash 4). It's not hard to believe that popularity played little, if any role outside of Mega Man until DLC started to roll in.