PCI cards, or at least some of those with analog ins and outs, are more prone to picking up RF interference (generated by various components in your computer), which will distort and degrade your audio. I had a POS "professional"

sound card which did exactly this. Noise floor was at times at -20 dB, which is outrageously bad. I don't think USB units in general are as likely to share this problem. But quality PCI cards shouldn't have it either.