I think popularity doesn't matter nearly as much as people think it does in most cases because now these days, Nintendo doesn't even run an official forum, and Namco-Bandai has a track record for not caring (TTT2 but still) - The best results for us to look at when it comes to additional characters would probably be the Melee polls, the Brawl fan-letter numbers (Where Ridley and Krystal had 4-5 and Masked Man had as much as Lucas himself), and the NSider Brawl Poll (Unfortunately, I'm the only one here who has an idea of how that looks like) which, if that all means anything, I think it gives Toad, Krystal, Masked Man, Ridley, K. Rool (To an extent, I don't remember much of these results even well; there's others who do better than me), Isaac, and a few others an upper hand but not by much. Especially since the rest of those poll results were included one way or another, and most as playable (Wolf, Lucas, Olimar, Ike, etc)
Unfortunately a lot of the other stuff came in too late (Chrom, Shulk, Palutena, etc) and would be added on their own merits, most likely, if they were included. It's also worth noting that Bowser Jr nor Paper Mario didn't have much of a fanbase until after 2007, which really sucks for them considering they're on the Top 10 almost everywhere I go.