Personally, I think the last of the G4s is a better option. The G5 may be faster, but I don't think it lasted long enough for Apple to engineer out the last few kinks. Plus the liquid cooling systems on the high performance models are booby traps with ticking clocks. And Apple kept changing the type of PCI slot included. That kind of architectural change means they never settled enough to really iron out the last of the kinks.
On the other hand, the MDD machines are at the pinnacle of G4 development. They are preceeded by four or five earlier revisions of G4 computer. By the time of the MDD, Apple knew what it was doing with the G4.
In much the same way that the SE is at a pinnacle of 68000 development, although some might put the Classic there. Personally, I think the Classic is on the downward side of that mountain. They reached the top, then looked around for ways to economize and headed back down the hill at that point.