I was using MOO2 as an example, since I have recently played it quite a lot
But as someone mentioned, having monsters change the habitability of the system (maybe even radiated == inhabitable for all, as in MOO3?) would be nice.
What I am suggesting, is to make the monsters a gaia force in the galaxy, which grows and develops at about the same rate, as empires would normally do on their own. Of course adjustable with initial settings, allowing for different skill levels of the players.
By this, I mean, if we took the krill swarm, at the beginning of the game, there would be several hives planted in the galaxy, which would develop a krill swarm usually at about the turns that the players would get their first ships out (i.e. they can kill all krill hives in the vicinity of their home unhampered).
The initial krill swarms are not extremely tough, but tough enough to give some chance to lose your first scout/destroyer. This would prevent the players going on rampage streak, destroying all hives/swarms even before tougher monsters would develop.
As the game progresses, a frontline between players and krill swarms would form, shaping the galaxy in its own unique way (i.e. there are "easy" ways, and "hard" ways around the galaxy). And players would have to choose to either go through krill-infested areas, or go head-on trying to battle well-defended planet of your enemy.
As the technology is being researched, and players' ships get stronger, that a single krill swarm is no longer a problem, the krill population should already reach critical mass needed to form large and huge krill swarms. Each posing risk to either single ships, or whole fleets. This stage allows players to nip away the outer "small krill swarm populated" solar systems, while having trouble getting deeper into the wild areas of the galaxy. It would also cause a stream of small krill engaging their planets regularly. (maybe add "krill migration" ? having to constantly fight minute amounts of krill would be extremely annoying. If, instead, there would be a regular small krill swarm migration into players' territories, that would simplify the problem). The technology level at this stage has reached an intermediate level (i.e. middle of the tech tree or so).
By the time the players' colonies have grown to the full potential, and they are about to advance into the last stages of the games, supermonsters would spawn from the current huge krill swarms. The type of supermonster would depend on the krill's diet, be that players' colonies, ships, or flora at their natural habitats.
Supermonsters can be treated as "quests", where player is set up to gain additional (possibly crucial to his plan) technology, and if the supermonster is ignored long enough, he can either degrade the wild planets to unusable levels, or go on rampage in one of the player's territories. Care should be taken when programming the logic, preventing such supermonster from outright destroying a single unlucky player. (i.e. after the colony is destroyed, retarget for a different one, on the other side of it's own habitat?).
Such monster evolution, matched to the player evolution, would result in several new aspects of the game :
1) planetary defences are commonly useful, and used
2) dynamic chokepoints, governed by monster habitats.
3) expansion dampening, smaller empires, high fleet reaction times, intense gameplay
Of course players should be rewarded for fighting monsters, and not just the supermonsters. Separate research tree, with several research techs requiring the player to capture and/or kill a certain type of space monster to progress further.
Would be nice if that tech tree would be normally hidden, and defined by the space monster properties, rather than hard-coded into the generic tech tree.
For example, with krill swarm, the monster tech tree would have a "stun net" research, which is a weapon mounter as a special on the ship, allowing it to capture a single krill swarm, if it is close to it. After the swarm is captured, you get krill swarm research, and follow up developments from it (i.e., for example, improvements to swarm missiles, improvements to bio harvesting, etc?)