If you go back and look at what was going on with UT99 in its heyday (2000-2003) there were TONS of populated servers offering custom maps and mods. Also, one of the great things about UT99 is that it was not a disposable shooter game--it was less of a game and more of an online cybersport; it felt athletic if you played it right. For example, there were competitive clan matches and 5-on-5 organized capture-the-flag matches where people used voice comm and played assigned positions--it felt more like an athletic cybersport than a disposable FPS in the same way that playing basketball or football doesn't really get boring. In fact, there are some hardcore UT99 players who still play CTF PUG matches to this day, because it was just so much fun. There are still tournaments:
http://www.prounreal.org/mlut/
UT 2003 really was a big mistake because the game play changed dramatically to floaty-dodgeyness. I remember the huge amount of anticipation that circulated in the UT99 communities in the months before UT 2003's release. Then it was released and almost everyone was sorely disappointed. Some people moved on to different games and the result was that UT 2003 damaged the franchise's player base.
UT 2004 was a great game in its own right, but not for the reasons UT99 was a great game. UT 2004 was good for the Onslaught game mod and Invasion, but it sucked for on-foot games (CTF, Domination, Bombing Run) because of the
hit-scan-based floaty-dodgeyness which is why you can still find populated Onslaught and Invasion servers but not CTF, Domination, or Bombing Run. Consequently UT 2004 had far, far less clan match activity and overall player counts than UT99.