Yeah, in the one case where I tried the wii virtual console with a game that was big in my childhood (Contra 3), it just doesn't feel quite the same. Noone's gotten an SNES controller quite right, either. So I hang on to a SNES to bring out every now and then.
http://www.retrousb.com/ has adapters to connect the original NES or SNES pads to either USB or a Gamecube/Wii. I've used their SNES-to-USB adapter and it works perfectly.