The Support Bases (former Auxiliary Gens) are meant to reward players for taking the offensive.
Destroying a support base will:
-Rewards team with resources. Grants 500 mass and 37500 energy, each second, for 14 seconds (7000 mass). Increases by 4 seconds (2000 mass) for every Support Base destroyed.
-Very high chance of temporarily stunning entire wave. Dooms, ACU Hunters, and RAMBOS immune to stun.
-High chance to damage HQ for 5% or 7% of total health.
-33% chance of spawning T4 Allies for team.
There is also a 60% chance one of the following retaliations will be triggered:
-Nuclear Strike: A small nuclear strike. Nukes will NEVER occur on the first Support Base destroyed.
-Boss Wave: Spawns YOLO strength counter bosses.
-Artillery Barrage: Calls in a 4 minute artillery barrage.
Airdrops are always triggered as a retaliation for every support base destroyed. All retaliations increase in strength for every support base destroyed.
On destroying all Support Bases:
-Will damage HQ for 10% health.
-Stuns wave for 30 to 45 seconds.
-Grants resources.
-Crashes HQ's power.
-Spawns mapwide storms that damage anything in range.
Support Bases are still a work in progress. Might add a few more random events and will be adjusting others, before adding in options for players to fully customize. Bases are a little too difficult to attack with ground units at the moment, and the rewards might not be worth the mass costs and risks.
As for the Monkey Lords not spawning, now that you mention it, I haven't seen any in a while. Looks like I accidentally disabled them when I excluded "counterintelligence" from the unit tables. I'll fix that next release. Thanks for the feedback!