Merchandising! http://www.youtube.com/watch?v=oNZove4OTtI
Seriously. One Piece merch makes a fucking mint for Toei. Naruto merch is just as big.
It's why there's always a new Super Sentai every year and Pokemon is nearing 800 episodes.
It's why Young Justice was cancelled (that and Cartoon Network being mismanaging idiots).
Pokemon is different though in that there's a very, very loose connection to any actual canonical story. It's more of there being a canonical mythos than an actual canonical world or plot. You can't compare pokemon to an actual adaptation like naurto or one piece.
Anhyways, based on the frequency of character appearances in the naruto filler, it seems to me that hinata and neji are by far the most popular side characters. Or at least, they were at this point of the manga/anime.
Kiba and Rock Lee appear quite a bit, too, but there's hardly any appearances of the Ino-Shika-Cho trio or Shino. Which surprises me, since Shikamaru is probably my favorite of the others.