I never thought about it like that. But then again, a lot of 2D fighters now are using 3D models, but just restricting them on a 2D plane. But I get what you're saying. Fans of 3D fighters don't get new games as often anymore, unless you're a Tekken or DOA player. A lot more does go into a 3D fighter, because they try to replicate realistic fighting styles. Not to mention, environmental interaction is a HUGE aspect in 3D fighters as well. I supposed it's easier to make 3D models on a 2D plane as opposed to just a fully 3D game.I'd say production hinders 3D fighters the most. Very seldomly does the 3D community get new games or event updates, with the exception of DOA5 of course.
Personally i think it would be good if Namco, Ninja, or somebody else to make a whole new 3D fighter series.