Even with the classic controller pro, I feel the control scheme to be lacking. In all reality, they should have released a replica of the N64 controller to use. I can't speak on using a Wii remote and nunchuck because I don't feel I'm versed in playing enough games to use it.
The graphics... don't get me started. Yes I completely understand that the game came out 13 years ago. I'd like to also include that my Wii is hooked up via component cables at 480p. I seriously believe that the graphics on the N64 version are a hell of a lot better even though I can't directly compare.
All in all, don't want to be disappointed? Go out and buy a N64 to play Goldeneye the way it should be.