Everything I can think of to improve the game has already been mentioned, but I guess I will just throw it out there anyway.
The ability to tell an asteroid that all of the seeds it produces should be sent to this asteroid. Maybe even down to a tree-by-tree level, say, if you wanted half of your seedlings to migrate to this asteroid, and the other to that asteroid. Going along with that, a patrol system might be nice, but I am not as sure about that one.
I think the aging of the seedlings and the trees would be good. Seedlings die after they reach a certain age, trees stop producing seedlings after a certain age.The trees dying would make people pay more attention to there first few asteroids. BUT if the trees are dying I think we should have some way of removing trees. Maybe not get your original seedlings back, but destroy them, somehow.
I think a disease idea would be kind of cool, but idk. Some Kind of random disaster, though would make things interesting. Make it something in the level, though. That way it is up to the level designer whether to have one or not, and what the frequency is.
A retreat option would be nice
I like the idea of each color of enemy using a different strategy, and I am really glad you already have that in the works.
I think that is it for now. I may edit in more if I think of it in like, an hour or so.