I've used both USB and PCI WiFi adapers. It's all the same really, what I don't like about USB based is that you end up sacrificing a USB port on a near permanent basis. Unless you have super fast WiFi 802.11ac and a crappy USB 2.0 port/adapter you won't actually notice anything.
For reference I have a Netgear USB WiFi adapter (802.11n) and a cheap 802.11ac USB adapter and they both perform equally well.
I also had a Netgear 802.11a/b/g PCI adapter which performed reasonably well. The drivers we the biggest issue as it required some bloatware to work well.
