My idea is simple. Instead of removing GLs, Xeno and Web from combat, simply make them more difficult to obtain. Require level 4-5 for an alien to get the hive 3 weapons, and require a level of 4-6 for a GL.

This way, people can still practice the use of these weapons without them being available before a counter is. By the time marines have GLs - devastating to spawning skulks - the aliens can easily have fades and lerks to guard the hive area. By the time the marines face webs and xeno, they can have the armor and welders to efectively counter them.

Me likey
Makes combat more complicated for new players though

Make it so Fades need some level requirement as well. The Fade is the on the top the Kharaa tech tree in terms of effectiveness, and you can get it at a very early level.

So, if GL is restricted until level 6, then so should Fades.

Won't this sort of force a linearity to all combat games?

Not neccesarily saying it's a bad idea. Maybe you just need to make level tiers.
AKA: At level 3 such and such upgrade possiblities open up for rines/aliens, at level 5 some more, etc etc.

I consider all of those valid options, and would have no problems to trying them out.