Aliens. Definitely Aliens.
I'm still not great with Aliens, and I'm still figuring out how to take down bases with them, but I like them a lot better.
They move so much faster. A marauder can fly faster than most human players can track me -- I can fly right into a pack of humans without being hit, after I'm there and messin' with everyone, well, that's a different matter. However, I get regen, and I can fly out in a similar manner.
Quake3 is still one of my favorite games, because of the speed and intensity. I also always preferred the gauntlet to the machine gun (I habitually switch to boxing mode and go for humiliations until I can get rockets or the rail, or the like). So, I don't mind the melee combat, or at least, I don't see it as a huge disadvantage, since it is pretty easy to get into range.
Playing as humans feels like playing a level of Quake1 filled with fiends and -speed turned on, permanently. Not a bad thing, because it is, in fact, good game ballance, I just like speed and stealth more than firepower.
Jeff