Popularity is a hard thing to gauge. Yes, Pokemon sells more, but Final Fantasy seems to draw more attention on polls, 'wishlists' and well...fanboys/girls following it. As well as Final Fantasy having more games than any other franchise in the history of gaming aside from Mario now (around 70 last time I counted).
But if we're just going by sales, yeah, Pokemon is #1. But then Final Fantasy is #2 again, depending on how you look at it. Dragon Quest pulls in the all time records of first day sales for games in Japan time and again, but the sheer size and number of FF games puts Final Fantasy in the #2 slot for RPG sales in Japan.
So again, everything is just how you want to label it.











