The PCI one takes its power seperatly from the motherboard whereas a USB one takes its power from the USB ports and is shared over all of the USB. That to me would be the only real difference I would think.
If its some sort of cabled system then this could be important as the signal loss on a USB system could mean, if the cables are long, that it doesn't work. Personally if I was setting up a permanent system I would prefer to use the PCI unit as it wouldn't be sharing its power from the USB together with anything else USB you have.
But then again thats just my slant on it and I haven't done anything like this.