The G5 is in pretty much every way a better processor, and even the lower spec models top the factory spec G4 towers. There's also the fact that the G5 can hold a LOT more ram-no G4 can take more than 2gb, while even the lowest spec G5s can take 4gb, most of the better ones can take 8gb, and the last generation ones can take 16gb.
The difference will be even more pronounced for you since you are using the lowest spec FW800 MDD, which is crippled by the 133mhz system bus.
While not a perfect comparison, everymac.com shows the G4 you have with a Geekbench score of 570, while the lowest spec G5(1.6ghz SP) has a Geekbench score of 918. The model your looking at scores 1692, or nearly three times your current MDD.
http://www.everymac.com/mac-benchmarks/mac-powerpc-g3-g4-g5-benchmarks.html
Hard drives really are not a big deal for the G5, since you're not scrounging around for NOS, refurbished, or used IDE drives and instead can buy new production SATA drives.
I still love G4 towers, but the G5 has some big advantages in many areas when comes to still being useable computers.
The biggest advantages I see to a G4 MDD over the G5 are the ability to take two optical drives(I know of few people who have used this capability in their MDD, although admittedly I do have one configured that way), lower power consumption, and better compatibility with older peripherals(i.e. external SCSI devices). You also can't put four hard drives in a G5 like you can an MDD, although IMO the ready availability of high capacity drives that will fit it(try finding a 2 TB IDE drive) more than make up for this.
G5s are also-in my experience-generally quieter than their G4 counterparts under normal loads, although admittedly do sounds like a jet about to take off when all 9 fans kick into full blast.
Finally, if you're into gaming or other graphics intensive stuff, G5s open up a much better selection of plug and play video cards. They also have an 8x AGP slot, where the MDDs only have a 4x slot, so the same will generally perform better in a G5 than in a G4. Some G5 cards(or flashed PC equivalents of them) will work in an MDD(see our ongoing thread about the ATI FireX3 Gl, which flashes to the equivalent of a Mac X800 XT, one of the best cards commercially available for the G5), although again take a performance hit relative to the G5 due to the 4x slot.
