the fundamental difference is that the quake engine is marketed as 'quake', 'quake2', 'quake3', 'doom3' engines. whereas the unreal engine is marketed somewhat separately from the game itself. its provided in smaller increments, which are easier to cope with. Its object orientation means that whatever you created for the previous version can generally be updated automagically, assuming you inheritted from the correct classes. you can more reliably upgrade from from one unreal engine version to the next, more frequently, than with quake where you would be upgrading from quake3 to doom3 for instance.
its just a more stable environment.
id make sweeping changes, and yeah, they get cool stuff out of it, but each and every time, everything else has to change, especially the entirety of your game code. Consider the changes you would need to make to port hexen2 to the quake2 engine, or to the quake3 engine. the unreal engine *still* runs uscript, and while there have no doubt been many changes, a complete rewrite of all code has not been required, as far as I'm aware (unline any of q1->q2->q3->d3 - q1->q2 being the least severe).
frequent minor revisions also mean more releases of unreal tornament. the lack of major overhauls means that much of what was available in the previous version is still present in the next. which means each release is more polished on initial release, rather than having to patch in lots of polish later.
Note how there are games released for UE3 before the respective version of unreal tournament was released. Conversely no id-engine game was released before or even during the year of the respective id game, despite the fairly close link between id and raven.
if I were a commercial game developer, yeah, I'd say the unreal engine is a safer bet. sorry. at least this is the impression I get.
on a personal basis, I still prefer id's stuff. I never was able to get the unreal editor to stop breaking my geometry any time I moved something.
my opinion, your milage may vary.