Given that this universe is pretty big, and that biotechnology will probably let us avoid terminal issues with biological bodies for a while, I would be inclined to keep a modified human body at least until emulations are pretty damn glitch free. There doesn't seem to be any reason to rush this.
Reading this article on requiring lots of processing power to emulate the snes accurately, made me think that we will likely have similar issues when emulating humans.
I'd imagine weird timing and chemical interactions being used by the brain as it is an adaptable system and might be able adapt to use them if they turn out to be helpful.
This suggested to me a few issues with no easy answers that I could see.