I agree, but not for your reasons. Stage 1 is biased heavily in the aliens favour, but no where near as heavily as stage 2 is biased in the humans favour. Stage 3 however I find is slighty balanced in humans favour, because of the cheapness of BSuits. Its far easier to rack up a few dretch kills for a S3 human, than it is for aliens to get a few evo points.
I think the reason for this is due to the fact that nearly all of the humans have some amount of money when they hit s3, and so none of them are completely unequiped and vulnerable to dretches. This is because they get money is distributed in a continuous way for doing any damage to an alien before it gets killed. Aliens however dont get this partial credit for killing lesser equiped humans because of the more discrete way evo points are gained. And so at s3 you can often end up with 3 or 4 evolved aliens, and the rest of the team dretches, who end up getting cut down again and again, helping the marines even more.
My suggestion for this is to simple move the aliens onto a credit based system, like the humans, with different aliens costing different amounts of credits to evolve into. I cant see any down side to this system, and it would do a lot to solve the imbalance of kill rewards for the two sides