I have an idea for attrition. It is based on my theory of how an organic Dyson species would work. I've had to rework it after version 1.20, but the core is the same.
First new thing is the seedling anatomy. I realize that the quality is comparable to cow dung, but blame it on my choice of drawing program (MS Paint). I hope it is interesting enough to take your attention from the low quality though:

The seedlings fly through space using a form of combustion engine, for which the fuel is created from water and various gasses (the oxygen is taken from the water). A lot of the energy is received by solar power, but the propulsion is combustion-based. The idea for this was partially stolen from Alien planet (see:
http://en.wikipedia.org/wiki/List_of_extraterrestrial_life_in_Alien_Planet#S).
The seedling is covered by a chitin-like material. A hole is quickly filled by the body fluids that contain some cells and fluids capable of repairing holes. The firing (yes, I noticed my spelling mistake on the picture) is done by a yet to be described process (perhaps we should leave it at that, in order to avoid technobabble) in the organ behind the "nose". The "nose" targets the shot and also contains certain sensory organs.
The seedlings have three senses: balance (to know what's down and what's up), smell (to find certain gasses) and sight (probably needed to detect enemies in space). They communicate with pheromones (or an equalivent) and visually. If a seedling runs out of resources, it dies.
There are four "sexes" among the seedlings. There are two "female" sexes, regular and defensive, and two "male", regular and defenders. The male is your ordinary seedling (see the picture). Both females are three times larger than the males. They cannot "shoot" with their nose, instead it is used to burrow into the ground and start "planting". Behind it there is a large "root" instead of the firing processing organ. They also have an additional, smaller, propelling organ near the base of their wings. That is turned the opposite direction and used to slow down when "landing". The seed organs are larger (in proportion to the rest of the body), and work fundamentally different.
When mating, the female calls for males to "seed" her. They release their seeds onto the female, and then burrow around her to aid her in gathering solar energy. The female collects the seeds with her collection organs. After that she lands and "plants" herself. Her body becomes the base of the tree. The two sexes each form a different type. The regular females form a regular Dyson tree, and the defensive females form defensive trees.
The trees produce a lot of the gasses needed by the seedlings, and take up the remains that they need for themselves. Regular Dyson trees produce all female seedling types and the regular males. The defensive trees produce defensive male seedlings.
Defensive males have an even more primitive "brain" than the regular males. They sit on their trees until given the signal to attack. They find a target and follow it until they ram into it. They have much larger fuel processing organs than the other males, and have three small "wings". These wings contain "fuel". When they ram into a target, they shoot their wings into it and then start an explosion, usually destroying both. A defensive male cannot land, and it destroys itself if it can't find enemies. That way the other males and the females can take up the gasses and materials for their own use.
So, here is how to add it into the game:
Each asteroid has an atmosphere. It is simply two variables attached to each asteroid that tells the balance of the gasses (burnable gasses and burnt). Seedlings take up the burnable and use it to move and attack. Thus each have a variable saying how much gas they contain. When the seedlings use gas, they exhaust burnt gasses. Those gasses are taken up by the trees, and turned into burnable gasses again.
This immediately adds a limit: a Dyson tree can only process a limited amount of gas per "tick", thus making the burnable gasses slowly decrease if there are too many seedlings at the asteroid. If you also make the trees produce slower if they lack the burnt gasses, you will force the player to maintain some seedlings at each asteroid, thus limiting amassing of armies further.
Then each asteroid can have an "earth" value. This slowly increases for each tree, but decreases when trees or seedlings grow. This should also go down (or grow slower) when the trees can't get the burnt gasses. Finally, you can have a core value which always slowly increases to a maximum value. Trees should use this for everything, meaning they will slowly drain the core if there are too many. Then you can have a much higher tree limit.
There are a few more changes and rules needed if you intend to stick to my theory:
* Defensive seedlings cannot gather their own gasses, they only send out used ones.
* Defensive seedlings do less damage the less gas they have left.
* All seedlings die when they run out of gas.
* Trees go into a coma when they can't get enough gas.
* There should be buttons for production of females.
* There should be a menu where you can chose what types of seedlings are to be selectable (so you can chose to move only males or all seedlings).
* A seedling's maximum gas depends on its size.
* The size of the wings also changes the agility of a seedling.
There are also changes and rules that could add more depth and fun into the game:
* A system for way points with rules (when seedling count exceeds X move new seedlings to asteroid Y) that they player can define.
* A rule system for production (stop production when seedling count exceeds X) that is also controlled by the player.
* More graphics! Examples: Visible flames from engines, visible atmosphere (colour balance can depend on gas balance) and more on that theme.
* More stats, such as agility, energy-efficiency and regeneration.
* An advanced regeneration system. Each seedling would have a certain amount of "fixing materials". When a seedling is damaged, it uses some of this to "repair". A powerful first attack might take a seedling out, but it could still keep fighting if it has a high amount of fixing materials.
* Background life. Plants that work like Dyson trees with resources, plant eaters (who know well not to try to eat Dyson trees), predators and perhaps peaceful passing creatures.
* Communication between seedlings (with pheromones).
I realize that it will take a lot to include all of this, but keep it in mind when considering limitations.