I recently loaded FCE Ultra GX v3.0.9 onto my Wii and was playing Super Mario Bros. I noticed while I was playing that there is way too much of a button delay going from the Wiimote to the game. I'm pretty good at SMB1, and with the Wiimote I'm constantly missing spots that I intended to jump from and player movements. It's pretty much unplayable for me since I typically run at all points while playing the game.
Another game where timing is everything is Punch-Out. There is no way to defeat Tyson unless your controller can handle the split second timing that is required.
I just played Super Mario Bros on Virtual Console and the response time is way better. The problem must be in the software somewhere.