It seems to me like "popularity" is the only bar in which most people seem to consider important. If it were, I think the first pass would have been much different.
I don't think it's unreasonable to expect Sakurai in the dev team to look, wholistically, at the roster and think, "We're nearing 100 characters, and are trying to make this the 'ultimate character game'. What big series can we get?"
Sakurai has stated this before. This is likely his magnum opus, his greatest work. If he adds a pass full of more completely-new characters to Smash, the crossover gets past 40, something it wouldn't if he stuck with upgrades, for example.
There's more to Smash than just adding "the most popular", especially when we're looking at what's popular specifically among Smash-fans. There's the saying that the consumer "doesn't always know what they want", or at least thinks they want what they want. With the scope of the game, I don't think popularity "doesn't matter" or something, but I don't think it's the be all end all indicator. Terry Bogard and Joker seem to acknowledge that imo.