This is mostly personal preference. USB used to be too slow to run a wireless card at maximum speed. That is no longer a limitation. You of course need USB-3 if you are are going to run 802.11ac cards at full speed. The PCI has the advantage of simple ability to put larger antenna on . The USB has the advantage of being able to extend it away from the case with a cheap usb extension if the case is blocking the signal.
I tend to favor the USB lately because antenna replacement advantage is not as clear cut when you consider mimo where there is a very critical dependance on the antenna size and spacing.