This is exactly what I came here to post. It's a shame, because FW400 was far superior to USB2.0. The problem lay with the peripheral manufacturers who didn't want to put in more expensive controllers and dual-ports on their enclosures. Heck, wasn't the iSight the only webcam for Firewire? No demand=no supply=high prices. FW800 was pretty much the same. Better tech, limited market, high prices, bang, whimper. I love that my old Mac Mini can transfer data between 3 daisy-chained FW400 drives much faster than it can transfer to a single USB2.0 drive, but the fact that enclosures are expensive and basically non-interchangeable with any of my other devices makes it a pretty niche market.
Thunderbolt will probably follow the exact same progression, right down to the "new" faster Thunderbolt. Sure, its PCI-E, but 95% of consumers don't know, care, or need that capability. They buy on price and availability, plain and simple.
One of the security failures of firewire was that it provided direct access to memory. In other words a malicious external device could gain complete control of the computer. Having your peripheral interface be PCIe is just as bad. USB for all its overhead is still more secure (assuming you finally fix some of the stupid windows autoexecute bugs)