How to make it different
I posted a VERY rough idea how to make the Alien Comm even more different than the Marine Comm here
My idea is this. Each Chamber and upgrade benefits the Comm as well as the players and changes his or her play style. Instead of just choosing a chamber because of the upgrades you receive why not make it fun/different for the comm as well. Each chamber would focus the comm on a play style and each upgrade would give the comm an ability as well.
Short of it:
Crag hive = Fortress comm, More defense but slower expansion. Gives comm a structure only heal and more armor to structures through the respective upgrades.
The other hives follow suit in a less than creative way. This was just to give the idea some form to build on.
It would be nice to also come up with an ability the comm gets from just picking the type of chamber. This would personalize each choice the comm makes and give the commander more room to develop play style the marine comm does not have. Marine comms are all about team support and front line attention. The Alien Comm is the "Gardener" and it would fit nicely i think.
What do you all think of the idea. Ways to improve the idea can be posted at the link.