In NS, the difference between aliens and Marines are CLEAR. They bother feel completely different. However, once you eradicate that difference, balancing will force both sides to become more and more the same.
I can see it now: Marines -> ranged team / Aliens -> Melee team
The alien commander is just a bad idea, and imo will most likely steam roll the uniqueness of each side.
I actually posted a suggestion concerning balance and differentiation that i feel goes with this in the suggestion forum.