Although I owned the NES version, its nowhere near as the original Arcade one. And slowdowns and all I still prefer the later, plus you can overclock it, run the bootleg or edit the source code to modify the speed of the CPUs directly on the source (so you don't have to overclock it every time you play the game, just don't post bugs with the modified exe).
And I don't remember fondly the NES version because at that time I thought it was exactly the same as the arcade one.