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
Hope this helps at least a little bit!
War produces veterans, wounded both physically and mentally. They have sacrificed for us.....and it is now our job to help these veterans, as they have already helped us in ways we will never know, in ways that we cannot fathom, and in ways that we take granted every day.