I can see few advantages of a PCI card other than most take external antenna which allows you to place larger antenna.
If you were to put a USB directly in a slot in the back of the machine you get the same issue. The case blocks the signal from the front, the wall blocks the signal from the back and since most people put them on the floor your desk blocks from the top.
Best option I like is to use A USB card and a USB extension cable so I can place the device where I get best signal, ones that can take external antenna are a added bonus. I also like it that I can move it to another machine very easy if I need to.
My favorite is alfa awus051nh. This is a dual band device.....The added bonus is this one is one of the best to use as a wireless capture device with backtrak if you are into that type of stuff.