This engine war is truly a flame bait waiting to happen..
Here goes.. I am a big believe in the id engines and prefer the general movement "feel" compared to all the Unreal engine games. Comparing those two games (you mentioned)is like comparing apples vs. oranges. They are two different games from two different development teams (that include art, modeling, texturing, level design, etc) that really don't have any interaction with each other. I would bet, that given enough time and energy, both games could look 99% the same and we wouldn't be able to tell the difference.
For now, the games based off the Unreal engine are going to look quite sweet and play well (they should, the engine is a few years old now). If you look at the track record of id engine games, you will find Half-Life, KingPin, Soldier of Fortune, etc. All of these games were quite good in their own respects, even with the outdated id Quake2 engine.
Quake3's engine is still pretty new (only Elite Force has it now), so it has some time before lots of developers catch onto it and make games from it. Soldier of Fortune 2 is coming out on the Q3 engine, along with Return to Castle Wolfenstein -- so we will have some time to compare Q3 engine games against the Unreal ones.
On a personal note, I prefer playing Unreal Tournament over Quake3. Unreal Tournament is a well polished game compared to Quake3, but Team Arena is what Quake3 should have been.
/me puts on flame-resistant suit.
vash