I'll comment on the weapons that I feel need improvement.
Laser - I've joked often about how "Nexuiz CTF" mode should be renamed "Nexuiz - Laser jump" because of how much that skill dominates any of the others in CTF. The advanced laser jumping players move way too fast. When they get going, it's difficult to stop them. Unless you are also an awesome laser jumper, or you happen to have a Nex or maybe a Mortar, then you are usually S.O.L. Even with a Nex or mortar, it's still very difficult to stop them.
My Suggestion - Reduce the max speed of players. There's no reason for them to move that fast. Or add landing damage...if they jump too high, too far, or too fast, they could take extra damage as soon as they land (even if they laser immediately upon landing). Rocket Jumping from Q2 was acceptable because it was balanced by the amount of damage that you received from using it. Because of that, it was not abused like laser jumping in Nexuiz seems to be. Perhaps the laser should take a little more damage from the player who is it.
Machine gun - This gun is frustrating because someone with very little skill can spray bullets at you and it's really difficult to avoid getting hit by them. This helps to ruin maps like Greatwall, IMO, where there are big open areas. Everyone in the base will use a machine gun and you get sprayed down with bullets within 3 seconds of entering the base. That is, unless you are a laser jumping god, which it appears only 0.002% of the Nexuiz community happens to be.
My suggestion - I'm not sure why this weapon is an instant hit weapon (don't remember the official term for that). A real gun doesn't hit instantly. There is a slight delay for the bullet to hit the target, even if it's in milliseconds. Giving the bullets a tad bit of delay would help. I'm not entirely sure what could help this weapon. The concept of it is that of a "hold down button and spray" weapon. Maybe look to real life to see why soldiers don't hold the trigger and spray bullets with a real machine gun. Maybe their accuracy gets worse the longer they hold the trigger. Maybe they run out of ammo too quickly. Maybe the gun overheats if the trigger is held too long. Those are some things to consider.
Mortar - Too powerful. Why do the stats show it lower than the other weapons? Because people don't know how to use it. That does not mean that it isn't powerful. I learned how powerful it was by playing and watching more experienced players (esteel, Dave) and watching demos of the better players (kojn). They all demonstrate how powerful it is. I've learned to use it more and more over the past couple of months. The only acceptable aspect of the mortar is the launch speed. In CTF, this weapon is very useful because it is one of the few weapons that can stop one of those speedy laser jumping freaks that move at 1000MPH away with the flag. The RL is way too slow for that. Other weapons are too slow or too weak to kill them at that distance.
My Suggestion Keep the speed as is, but slow down the reload a tad. Secondary fire is fine the way it is.
Another alternative - Limit the max-speed of travel for CTF players (as mentioned above). When they move that fast, it's difficult to stop them with anything but a Nex or a Mortar...or *maybe* the electro if you're lucky. If that happens, then the speed of the mortar projectile could slow down a tad and make it more balanced with the other weapons.
Rocket Launcher - This could use some slight adjustments .I would drop the power of this weapon slightly, and then maybe pick up the speed of the projectile slightly. Nothing huge...just small tweaks. Also, the right click detonation should be a little weaker than the primary fire. There has to be some trade-off for right click detonation...because it is really too powerful. The RL would be more powerful if people knew about the right click detonation feature (MANY people don't use it). Maybe if the speed of the rocket was faster, it would be harder to time the detonation?
Finally..
I think it would be great if there were some test version, or a test server, or a mod or something where we could test out differen't variations of the weapons. This would help to workout the details of weapons balancing. I have no idea what this would entail just yet, but all of these suggested changes are theoretical at this point. I don't know if my own suggestions suck or not, and it would be great if I could find out somehow.