I would go PCI if I had a choice. I realize most new computers have 8 or so USB drives, but those are with extentions. You usually only have 4 or so on the back. Two or three are already taken up by mouse, keyboard, and printers, then if you want do sync your PDA you take another one. So while there are plenty of USB bays to go around, you can never find enough IMO - and I personally don't like connecting them to the front of the computer unless it is something like a thumb drive.
So for convenience I would suggest PCI. As no one wants to plug / unplug devices you don't know what they are to because you run out of spots in the back of the computer. And in the future there will more and more devices using the USB drives - so save yourself the headaches and just get a PCI one.