PCI tends to give less installation issues then USB, although I've never had any.
USB adapters have embedded aerials which allows you to place it for better radiowave transmission/reception.
Most PCI aerials are stuck behind a metal (bad news for radiowaves) PC casing as well as loads of wiring. However some aerials can be removed and replaced by an external aerial of higher gain (sensitivity) or comes with one in the 1st place.
More PCI adapters then USB cater for the better WPA wireless data encryption method.
If you have a "weak" Power Supply Unit (PSU) in your computer and have added more hard drives, etc, another PCI card or USB could stretch one of the PSU's powersupply "rails" beyond the limit and cause unstable operations.