For 1080p, Nearest Neighbor isn't a very good option for NES/SNES resolution. Multiply the standard 224 height by 4 and you get 896, using only about 83% of screen height. Multiply by 5 and you get 1120--oops, we've gone overboard. HOWEVER, scaling by 4.5 with minimal possible blurring should work pretty decently, and I'm guessing SNES games do something like that. Whatever it is they're doing with SNES games, it's puzzling they're not doing the same with NES games; the vast majority of games for both used the same resolution. For Gamepad a simple x2 scale would work decently, and use 93% of image height. However, the compression it uses for all imagery is always going to harm the clarity of VC games.
Here's an image I made quite a while back showing off the 4.5x as I mentioned above, and I think unless you zoom in it's hard to notice any blur. The image on the far right is if they wanted to match the actual old 4:3 TV aspect ratio, rather than just going with the 8:7 pixel ratio those systems produced.
http://i.imgur.com/C9idWq4.pngAs long as we're complaining about the NES image quality, though, it's not just that they're blurrier than SNES games, they're also darker.