I do find it a problem that the internet is full of mails from people who say that it runs very well on G5s. I think it's important to change this message fast and make people aware that upgrading while running a G5 will give you quite a few headaches.
I find it hard to believe any of the problems you reported have got anything to do with your machine being a G5. Sure there will be bugs, and sure they will not be apparant on all machines, but whether cmd+S works surely has got nothing to do with processor family. (Have you checked whether the key command for save is actually still there? It's just a configurable key command like all the others. Maybe it got overwritten by something). The nasty thing in your situation is, that there is no use in reporting the bugs as long as nobody else finds them since you're running an unsupported system. But the specs on the Apple site told you that already.
The fact that Apple doesn't support the G5 for Logic 9 is simply due to the fact that they consider that processor too old (which means they can't guarantee it can keep up with everything they advertise about and they don't want another lawsuit like with the G3+OSX+DVD class action), while the fact that Logic 9 is still a universal binary shows that it has nothing directly to do with the Intel transition and they actually unofficially still WANT it to work on a G5 (just not in the juridical sense).
Now if they didn't test it thoroughly on a PPC there's bound to be some G5-specific problems but they won't be as high-level as cmd+S not working. More like timing problems and things like that.
So, if these really are bugs in Logic than Intel users will find them sooner or later too.
Maurits.