EDIT: split from here
I added a ground level tech "Domesticated Mega-Fauna" that's now required to raise monsters from the monster nests.
If you don't have the tech, but colonize a nest, it will be safe, but produce no monsters until you get the tech.
In my current game (or play test) I put an outpost on a Hydra Nest and after a few turns I got Hydra which were on my side, but which I couldn't control. I could rename their fleet and combine two hydra fleets into one. But, when I combined the hydra into one of my normal fleets I could control the combined fleet - it had the name of my normal fleet, but had a monster icon for the fleet. If they are uncontrolled they should not be combinable with a normal fleet. (Renaming should be allowed)
My point though, is that there should be a technology - called "Trained Mega-Fauna" - to give control of monster fleets.
Further technology could give bonuses to the monsters controlled by the Empire. The rate of spawning could also be increased.
I had another idea. A ship part could give the ability to combine monsters onto a fleet and give control of the monster. If the ship is destroyed the monsters become uncontrolled again, until another ship with the monster control part joins the fleet. The best thing about MoO2 was the odd things you could put into ships. The ship part could be a 'monster prod' - like an oversize cattle prod. A better one could be a 'whistle' or some kind of pheremone dispenser.