You can be sure that I am not an expert on the subject, but I listened somewhere that the way G3 and G4 handle "Code" is different than G5 in that Little Endian/Big Endian Game.
AFAIK, that's only for virtual machine programs, which make use of endianness switching. G5 can't switch endianness like that (which is why, at same clock speeds etc., VirtualPC is slower on G5s), but that's about it.
In regards to Instruction Set Architecture (ISA), there are no concerns, as well, as the G5 contains a superset of earlier ISA implementations of earlier PPC processors. (Not too many new functions, though.) That's what the IBM docs reveal, anyway, last I checked.
Above all, to my knowledge, the main issue with the G5 is "mere" lack of drivers. Not sure which, though. Motherboard(s)? NorthBridge? G5 CPU recognition itself (just like how OS 8.6 doesn't recognize most G4s, supposedly)?
Anyway, I'm no expert, either. But looking at how other systems (GNU/Linux, BSD, MorphOS) boot into both G4s and G5s, they might be a good start. Also, starting with earlier G5s certainly sounds much wiser than with late G5s, that's for sure.