I'd have to agree with the theme here that others are talking about. Theres just too many buttons for it to be fun with arcade controls. There are always exceptions however. Like I currently use an N64 emulator for the "The New Tetris" game thats on N64, and I control it with my arcade controls just fine. But that's only because there are 3 buttons that you use in the game. So is it technically possible to do the N64 thing with an arcade, yes, but it is friendly or intuitive, depends on the game, but usually no.
On a side note, I have no problems emulating SNES, Genesis, Nintendo and anything older. I especially enjoy playing NES on mine, and it works fine. Thats the general point where I stopped trying to emulate anything newer though.