I'm sure that in the entire technical scheme of things, there's a difference. However, I've had a pci usb card installed and then removed it (only to whish I left it installed). When I had things running from the pci over the usb off the motherboard, I didn't notice any difference in speed or performance. As for wich is better, well, based on my experience, I can't say one way or the other wich is better, as I saw no difference between the two.
There's some good reading on it
HERE from Wikipedia.
Hope this helps at least a little bit!