I don't know if someone already answered this question... I didn't want to read through all of the responses... but maybe this will help.
When the IBM PC was first spec'd out the designers saw a need for expansion slots to accommodate features that they either did not want to accommodate (e.g., modems) or which they had not foreseen (e.g., wireless LAN adapters). The initial expansion slot designed by IBM was the ISA. Naturally, technology marched along and pretty damn soon IBM recognized that they had made a major boo boo by (a) not making the ISA slot proprietary and (b) not making it more capable, so they came out with the IBM MicroChannel. About the same time the rest of industry adopted the EISA (Extended ISA) slot.
Time marches along and eventually the industry realized that the highest bandwidth application (video) needed something more, so you saw the introduction of video specific slots like AGP.
Eventually, because no doubt all this was confusing as heck to consumers, they settled on a new standard known as PCI. Naturally, this has given way to even more capability such as PCI-X 8 bit and PCI-X 16 bit, once again to accomodate the incrediblely kick ass video that no one foresaw.
Everything goes through the buss... firewire, USB, these are just technologies to more easily accomodate devices such as USB battery chargers and firewire soundcards because people... for the most part... hate having to break into the case to plug an expansion card in, and I can understand why. What if the damn thing breaks!! Furthermore PCI slots can be 3.3 volt or 5 volt (or both) and it requires a degree of technical confidence to mess with.
Nonetheless, firewire and USB introduce bottlenecks. The absolute, bar none, fastest way to get data to the buss is to plug directly into it.
PCI will only be dead when it goes the way of the ISA buss. And that day has not yet come.