IMO, Quake 3 had a more satisfying to use base weapon set than UT2004's and the movement goes well with the weapons.
But that's where the pluses end for that. UT2004 has more weapons, a flexible menu system, is easier to add custom content to (the quality of the content itself is pretty awesome if you know where to look too), has better bot AI, has a better editor, more gametypes that are fleshed out, and better graphics. Also, I think the net code's slightly better. Even the weapons which I just took a crap on earlier have the saving grace of more options simply with the primary and secondary fire they each have alone. PLUS all the hidden third modes of fire such as the Shock Combo.
And that is why I don't play Quake 3 NEARLY as much as I do UT and UT2004.