It's mostly a matter of bandwidth. PCI shares the data path across all peripherals, where PCI Express is point to point, and nothing else shares that data link.
PCI Express bus is not directly coupled to the processer, and it has direct access to memory. Here's the long version:
http://www.anandtech.com/news/shownews.aspx?i=21822
And here's another article that covers all the buses (sorry for the bad play on words):
http://www.hardwaresecrets.com/article/190