I think it would be nice if the aliens had a "Commander" also, but with a different twist.
Some Ideas as to how it could possibly work.
The alien commander, unlike marines, isn't something that players may start with early in the game. It's an upgradable feature that takes about 30 or so res..
When a player reaches the res requitements, he or she may mutate with and into the hive.
The benefit of a player doing this is that now, he/she has direct contact with the Hive's knowledge and may communicate it to other players.
For example:(possibilities)
When inside the hive, players can only see an area around their teammates, and may "Hear" an infested area when their mouse is over it.
This makes marines extra cautious, about proceeding into an infested territory while encouraging stealth(sneakiness).
Infestation could be fought with flamethrowers, without alarming an alien commander. Only an attentive commander would notice parts of their visibility is slowly fading away.
Also, I think it would be nice if an alien commander had the ability to give waypoints, and to organize groups without calling them squads.
This way, in NS2 you'd find more aliens attacking in an organized/ intelligent fashion, rather then a single stray skulk being caught with his pants down or aliens just all going to a highlighted area. It could encourage teamwork and tactical teamplay when dealing with marines..
But these are just some incomplete thoughts =o maybe someone will think of somethin better
