Well, since I now have both of them installed to my PC I can see the differences between the two. [side note: I'm not sure if the original UT '99 and UT '99 GOTY version differ any, I will base this from the the GOTY point of view]. This isn't for me to say which one is better or not, I just wanna point out differences I notice.
-They pretty much have the same game modes. The only one that Q3 doesn't have is Assault which would have probably been a great addition. The settings for UT have more options and Q3 is more straight forward.
-While UT '99 lets you pick a skin and face for your fighter in a well organized manner, Q3 has them in a 'Fighting Game' style without any type of in-game customization although you can pick what color or skin you want without going through a list of assortments back and forth.
-The maps that each of these games have are pretty fun and well made. The UT '99 maps can sometimes cram the fighters in certain areas making it real intense at times. The Q3 maps are a little bit more wider but keeps the fighters at what I would like to call, 'Fragging Distance'. I don't really care about maps that let you swim or not, or if they are bigger then the other...As long as you can frag.
-UT and Q3 have different game speeds obviously. While both game are as competitive as each other, they do serve their purpose for certain types of gamers. The maps in each game are designed to correspond to the speed, physics, etc. IMO. Since I don't really know much about this I guess I'll send here.
-UT and Q3 have similar weapons while UT seems to have more weapons than Q3. Q3 weapons are more straight forward because they lack secondary fire options making. UT weapons technology, the secondary fire for most guns are Primary in Q3, like the Pulse Rifle. The Pulse rifle is basically the Plasma gun and the other gun that shoot the bolt of lighting into one gun.
-I like these game the same. They both entertain me, they both have blood and gore, and they both kick ass...[END TRANSMISSION]
Thanks for reading my comparison guys!