Your Ninten could use a lot of work. Your skin and shoes seem to be the only parts that fit into the Smash 3 style - the rest looks like the original textures having been oversaturated. Keep in mind that just because Smash 3 (and Smash 4 for that matter) are more vibrant than Brawl, that doesn't mean they are super saturated with colors.
I tried asking you what process you used to resize before (not just the program), but if this is the best result that paint.net is capable of, I'd suggest switching to GIMP (for free) or Photoshop. Hell, I'd suggest switching to one of those two regardless, because that's what all of the Smash 3 and Smash 3C project files are created with, and it would be easier to cooperate.
It's coming along well, but I still think the pant seams on the side look awkward. The black line just kind of ends, yet the white one goes on all the way. Something about that just rubs me the wrong way, pal! Don't forget to adjust the inside of his sleeves, too.