I enjoy both games but I regard UT99 as having the best overall game play. When I want to play CTF it's UT99 PUG matches for me. However, I do like and I do enjoy UT 2004, but for different reasons. I enjoy UT 2004's Onslaught and Invasion Monster Mash-RPG games.
I will say this. If you look at online multiplayer player counts at a given amount of time after the release of each game, say three years after release (that's 2002 for UT99 and 2007 for UT 2004), there's no question that the UT99 player counts trounced the UT 2004 player counts, especially for the core game type Capture the Flag. The same holds true if you look at player counts two years after release (2001 and 2006, respectively). So which game was better? I think the player counts data speaks for itself. Consequently, UT99 also had much more organized clan activity and a stronger online community.
Let's hope that UT3 is as successful as the Original. Sadly, I'm skeptical of that. I like the game play in the Beta Demo, but you can tell that the packaging of the game has been "consolized". The User Interface really isn't all that awful, but what gets me is the god-awful server browser. If the final server browser isn't at least as good as the UT99 server browser then Epic has insulted the UT community as far as I'm concerned. The UT3 browser should be as functional and as feature-packed as both the UT99 and UT 2004 browsers combined. I sure hope that it's dramatically improved from the POS that came with the Demo.
I was real enthusiastic about UT3 and although I liked the game play of the Demo, the issue of the crucially important server browser (players' window to the online multiplayer world) has dampened my enthusiasm. They aren't including a built-in IRC browser, either, which is a huge mistake since the lack of it will make it harder for people who know nothing about IRC to meet and get involved with the clan community.