UT.
Netcodes not the best, but it handles lag the best, IMO.
Graphics lack some of the neato effects of Q3, but manage to look nicer, especially for realworld type maps.
Q3 needs hella fps, UT is smooth with 30+.
Q3 has bad interface, UT is simple yet powerful.
Q3 has some neat sounds, UT has as good(with mutators even the same)sounds. UT simply does music better as well.
Q3 hasn't lived up to the mod hype(the only reason I bought Q3), UT has a bunch of very good mods(RA:UT, Infiltration, Strike Force, Tac Ops, U4E) and hundreds of mutators.
I've said it before, and I'm saying it again, Id makes very good engines, but they don't know how to make a game!