While I prefer sprites to 3D (I don't need to bust out 3rd Strike or Marvel 2 gifs, do I?), it's really all about art direction. Injustice and SF4 look like shit because the art direction is ugly and bad. Compare to Marvel 3, which has an vibrant, colorful, almost cel-shaded look. It looks incredible!
Everything I've seen on the internet leads me to believe that I'm one of the few out there that likes SF4's art style/direction.