PCI is very slow compared to AGP though, about 15 times slower than 8x AGP in fact. This does affect game performance in some cases - any time you can't fit all the data onto the GFX card's onboard ram you're going to get horrific slowdown (it's bad enough with AGP). Also depending on the GFX card it may be unable to support holding geometry in video memory, if so you're going to see a large difference in performance vs a similar card on AGP. Given games are using more and more video memory for things this is only likely to get worse. One of the main reasons for PCI-E is it's faster and lower latency than AGP - which is becoming a big issue.
AGP Vs PCI
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