Reflections Lost on a Dark Road/WMG
The microbot swarms are working for another group of survivors in the "Space Hulk" dimension.
They're stealing power from functional electronic devices. While they could be using it to power themselves, they could also be gathering it to transfer it to a main ship to keep the ship running and the survivors on board alive.
The "AA" psychics are in a Cuckoo Nest.
What better way to deal with a world full of metahumans? The Hive Mind learned its lesson with the Nerima Wrecking Crew - abducting Ranma and his allies simply made X-Com aware of Supernatural Martial Arts. Why do the same to demons, magical girls, garage super-scientists, etc... when all it takes is a few subtle memory tweaks and a hidden Ethereal or two to make X-Com lock up all of Earth's native superhuman assets and drive them insane by insisting they're insane - and them and their tasty DNA will remain safely on the moon base until the aliens invades en masse. Nice Job Breaking It, Hero.
- Doesn't work well; the aliens' experiments (including the free range psychics) are far older than the six months or so since X-COM and the Mind discovered the Nerima Wrecking Crew, and it's likely that X-COM has been dealing with the psychics since before the Mind considered X-COM an actual threat; rather the aberration of the abilities of the Neriman martial arts communities moved the Mind to act unusually in that case. Of course, that doesn't change the fact that stuffing all the powerful psychics you can find in a loony bin on the moon may still be a handy way to drive the sane ones over the edge...
The aliens are "a cult of addiction in the guise of a species".
When the Hive Mind started conquering, they were just the Sectoids, an empire of mad scientists who enslaved and experimented on other species. Then they tried to enslave the Ethereals and lost. In the process, the Ethereals became as amoral, bloodthirsty and entitled as the Sectoids. After the Ethereals seized their databases and technologies, they continued conquering and enslaving and experimenting due to the xenophobia they developed in the course of defeating the Sectoids. If Humanity doesn't start caring that they're becoming exactly as monstrous as what they are fighting, they will simply take the Ethereals' place atop the hierarchy and continue the cycle. This might even be an intentional element of their civilization: a Darwinist Batman Gambit - lose to them and become their cattle, defeat them and make them even stronger as their new leadership. Heads I Win, Tails You Lose.
The aliens are the Anti-Spirals.
...Only smarter. Instead of trying to break the wills of the spiral races, their attacks are carefully tailored to make the defenders break their own. You and your fellow soldiers are cannon fodder; don't cling to life when there is a mission to accomplish. Your loved one could converted into a Trenchard at any time; don't get attached so watching what's left of them suffer doesn't break your concentration. There are no super-heroes, just psionic puppets; lock them up and torture them so they can't get in the way. Your ethics prevent you from learning about your enemy's capabilities; abandon them so you can tear secrets from their flesh. Your strongest soldiers have brutalized themselves for their entire lives to become strong; Misery Builds Character, and everyone should embrace it. The result is a species that could never understand Spiral Power.