SF3 > CvS2
more frames of animation. More consistancy between all the characters. Cvs2 has sprite rips from SFA and Dalkstalkers. CvS1 would be a different comparison, the High Res Backgrounds and special effects in CvS1 was awesome.
SF3 by far, although I like Eagle's modern sprites. I've always wanted to see him and other SF1 characters like Joe or Geki remade with modern sprites.