I have a Belkin USB 2.0 5-port PCI card (4 ports at the back of the pci card and one facing internally) and it works without any problems or drivers in XP and Vista. Link
I guess throughput based on what I read that PCIE is supposed to be faster than PCI. I cant speak from experience as I've never tried a PCIE USB card. Probably also depends on what slots you have free/available.
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