NS2 has an alien commander: this is one of those brand-new areas of the game that isn't covered by the ground layed by NS1.
The alien commander's role is that of "cosmic gardener", one where he is dreamily playing with the environment to do powerful, slimy things. I don't want him giving orders to other aliens - that would be too similar to the marine's "command and control" setup. Also, aliens move so fast and with so many different movement modes that clicking on aliens at all wouldn't work well. As "gardener", it would be cool if the alien commander was interacting directly with the environment. So I had an idea about him being able to create clouds of "pheromones":
Pheromone: A chemical substance produced and released into the environment by an animal, esp. a mammal or an insect, affecting the behavior or physiology of others of its species.
I have some ideas about what I wanted to do with these, but before I taint your imaginations, perhaps you had some ideas? How do you find yourself wanting to interact and communicate with your team, and environment?