Really? I had a 6 button pad and SF2 for my first PC-Engine DUO. I didn't think the pad was that great. I definitely preferred the SNES controller and SF2 Turbo on my SNES.
I like the Avenue Pad 6 so much better than the SNES pad. The SNES pad has a D-pad that is not well-suited to fighting games and the shoulder buttons suck. Sure, it was the best stock controller for SF2, but once the Avenue Pad 6 and the Genesis 6-button game out it quickly became the worst 6-button pad for the game. People who prefer the SNES pad to other 6-button pads are, IMO, in the distinct minority.
Sound wise it doesn't compare to the SNES's SPC chip. I don't know what you mean by palette either. The SNES hardware had greater color resolution. I mean it's still a nice port of SF2 for the PC-Engine. You can have your favorite though. Mine is the CPS1 version.
Music-wise the SNES version is better, but the audio samples are actually a little clearer on the PCE. The SNES audio chip did lots of filtering, making the voices all sound muffled. The PCE has the best voice samples of all the ports.
And really, the background scrolling is a nice graphical touch, but if you're really buckling down to play the game you're not watching for background scrolling.
If you haven't checked out Black Tiger's comprehensive comparisons, go here and immerse yourself:
http://www.superpcenginegrafx.net/sfiice_comparison_main.html