The Nexgun is used most because it is powerful and it can be used for sniping as well as closer combat. Therefore, it really doesn't have that many limits compared to other weapons. As a comparison, the RL is powerful, but it launches more slowly and you can accidently kill yourself with splash damage if you're not careful.
I know the Nexgun is a knockoff of the Quake Railgun, but I wish that it would be split into two offshoot weapons. One of them would be for a less accurate and less powerful run-and-gun type of weapon, like a mini-rail gun with a little less power and faster reload than the Nexgun. The other one would be a legitimate sniper weapon. The sniper weapon would take longer to reload and would require that you are standing still to aim well. It would use up more energy points. It could even slow down your speed while you are using it. It should be intended for sniping, which should include some downsides. Right now, there aren't that many downsides to sniping with the Nexgun, and it is extremely powerful, so lots of people use it.
It seems like a lot of things in Nexuiz are taken from Quake. I think Nexuiz could be more enjoyable if it became more unique and less quake-like. That was my thinking when I made the suggestion of removing telefragging[/url]