They should also take into account the balance of power on an asteroid and attack targets based on that too
Perhaps you could let the user control the target? That way you don't have to program an AI to be super intelligent about it (otherwise there will always be complaints, right?). Maybe you could do this by adding a prompt when you move seedlings to a planet with enemy units on it (after having discovered it) to select to attack seedlings, seedling trees, bomber trees or to just let the default AI as it is now do its thing. The last option would be best for when you have large swarms that would be most effective by just going after whatever is closest. And then allow the user to re-attack the planet (select all or number of seedlings then allow clicking on the planet they are currently on) so that the user can change the seedlings tactics.
Since doing this would make gameplay a little more complex, perhaps you could add an option to enable the tactics function and have it set off by default. This way the game will appear just as simple so as to be attractive to the beginners and more casual players, and allow for more advanced play to more established players.
Sorry for just jumping in. I just started playing this game and absolutely love it, but like others have said, it has a huge potential for growth as well without making it overly complex and daunting to new players and with enough room for more advanced strategies and if possible I'd like to contribute.
(Oh and last thing, perhaps in the 'How To' section you can add that both tree's require 15 seedlings to make, that trees grow to produce more seedlings/bomblings, and that a certain number of seedlings are needed to take over a hostile planet.)