"Popular" is the only term you've really addressed there, which is also misleading since the demographics of the two sales figures may or may not actually overlap at all -
Brawl being a game for long-time or at least more-than-cursory fans of Nintendo;
Wii Fit being a glorified daily exercise tool. One of these appeals to a wide market beyond those people who would actually give a rip about who's in the next
Super Smash Bros. game, as demonstrated in this very thread as well as across the web in general following the announcement. "Popular" in sales means nothing if no one looking forward to SSB4 really cares about it. Obviously there has been some positive reception to this as well as negative, but 'most every fan seems to agree that there are about a hundred and one characters who need to be up for inclusion first.
Her value as a "character" is really next to nil. Most of the representatives taking the stage in SSB have some semblance of nuance, personality, or expression; whereas the Trainer is literally
meant to be a mostly-devoid of personality robot in the form of a visually appealing woman who can give simple tips and coach whoever's on the balance board. Mario has never had much development as a character but he does have an interesting design and is usually quite expressive. The red cap alone is iconic enough that it's used as... well, an
icon. In contrast, I wonder how many people watching the reveal trailer would have known who Wii Fit Trainer is at first glance without being explicitly told?
"Franchise"
is pretty generous for a character with one and a half games to her name. This isn't a huge deal in light of characters like the Ice Climbers and R.O.B. making it in, but the majority of characters in
Smash can boast of at least a couple games in their respective sources, and I think the lack of being part of a long-standing series is part of the "wait, what?" reaction I'm seeing to the Trainer.