First, I would use PCI over USB any day.
It may be because they are trying to standardize on USB.. it's pretty much universally supported now, whereas laptops, embeded systems, and macs don't support PCI. It's also easier install, and easier to troubleshoot when it's "plug it in & load the drivers" vs. shut down, take of side of case, find appropriate slot, plug it in, etc.
USB takes up less space.. you can have 127 devices per USB controller.. PCI you can have 5 devices or less (some PCI cards that don't like to share resources, and if you plug them in the wrong place, the system board forces it to share it with another slot, making that slot unusable and causing weird issues if that's where you plug it in). USB is hot-plugable so you can plug & unplug it on the fly. Also, I believe USB devices take up less resources than PCI.
On the other hand, USB is less stable, and way lower bandwidth than PCI.