Mario, Sonic the Hedgehod, Kirby, and Donkey kong are still 2d games and are arguably the worlds most popular games. And if you hate Nintendo, there's still Marvel vs. Capcom, Mortal Kombat, and Street Fighter. All 1st or 3rd party games. I personally think a martial arts game like Dragon Ball would be held back by a 3d system. Like I said, ESF is a big step in the right direction but there's still problems playing a game like ESF with a controller.
However, a game like Bf3 is designed to be 3d. There have been extemely popular side-scrolling and top-down shooters from both 1st and 3rd parties that got immense claim. Even now, Megaman X is probably one of the best platforming and/or shooters that I've ever played. The side scrolling may limit certain aspects, it delimits what you can do with the guns themselves.