Okay, this probably sounds dumb, but I've been playing Nexuiz for about 2 months and just now got around to turning off mouse acceleration. Wow! What a difference. I can actually hit people with a Nex sometimes.
Oh, I could always snipe from the other side of the world using a big zoom. But at a medium range when the enemy is moving around and knows you're trying to shoot them, it's much different. You have to move your mouse quickly and accurately. Mouse acceleration makes it very hard to do that.
Anyway, if you don't know about this, it is in your system controls/preferences or in your mouse driver settings. It's different depending on your OS and mouse, but dig around until you find it and switch off acceleration. Your aim will quickly improve.