With Apple's switch from FW400 to USB2.0 as the interface for its iPod line, and the elimination of FW800 from all but the high-end MacBook Pro, I'm wondering whether it makes sense to invest in yet another FW400 drive, or if it would be better to go with a USB2.0 drive at this point?
Apple is not abandoning FireWire. Not by a long shot.
The reason they switched to USB 2.0 for the iPod is due to size. FireWire requires a separate chip to control it which would ad size to the iPod. USB 2.0 can be integrated directly into the circuit board of the iPod allowing them to achieve the slim size the current iPods have.
If they really were abandoning FireWire, it would not have made it's way onto all of the Intel Macs and FW800 would not be on the new 17" Intel MacBook Pro (USB is owned by Intel and Intel has never supported FW previously since it's a competing standard).
I'll bet you one shaved duck that the new Mac Pros (PowerMac replacements) will still have FW800 ports when they are announced.
The problem with USB is that it does not maintain constant data transfer speeds. FireWire is more stable in that regard (and thus the better performance). If you can, by all means go for FireWire.