I've played through the game. It's a generally excellent game, but there are a few simple things that would add a lot to the playing experience, and the replay experience.
Firstly, when playing with large maps, and large forces, you have to repeatedly select and click on planets to gather enough forces to attack an enemy. The game is slow paced enough that this isn't difficult, but it gets repetitive, and breaks up the relaxing flow of the game. You should have some sort of option like, if you triple click, you can select a circle of planets, and tell them to send all of their units to a set point. Rally points are slightly complicated, but if you just expand the current mechanism to select different units, it should be simple enough.
Plus, whatever algorithm controls moving, it should be set to avoid enemy planets if possible. It's annoying hastily sending some troops to aid a faraway battle and seeing an enemy annihilate them. And after that first time, it's just more clicks to get them to go where you want them to go.
The strength/ speed/ energy selection thing is a bit awkward to select. It could be faster. I suggest you connect scroll/ right click to a f/e/s icon, which would allow you to select one kind and send them off with a normal click. This would make the strategy of removing all strong/ fast ones after opening a hole in an asteroid for the energy ones easier.
In the game, I'd often set myself challenges to make it more fun- like, on event horizon, I built up a force strong enough to defeat the enemy counter attack on the main asteroid, and then quickly take their planet. I'd love to see distictive messages from the mother tree when you conquer places in different ways- crush everything, rush to objective, use a lot of dysons, use a lot of defence trees- signs that the mother tree cares what I'm doing. Some messages from opposing mother trees would also be nice- you will regret defiling our garden, growers forgive us for what we are about to do, etc.
The difficult of the game is very mild. In almost all missions, you simply have to build up a large force and rip through every enemy. This is why the above mass select thing is needed on large missions. It would be nice to see some optional minibosses- say, large planets with good stats, good flowers, that the mothertree orders you not to attack, because you'll be annihilated- like the giant planets on the mission where you get the laser mine. Give them an order not to attack unless 10 of their units are destroyed- a serious assault- and then attack with a very aggressive AI. An optional challenge, that people who want it can take.
An optional mode where you have random events would be fun too. So, say, a solar storm, where everyone gets instakill. Passing comets with tree slots*5 weak units that appear late game, and try to take over your carefully hoarded empire, or the enemy's. A flash of light that temporarily removed the fog of war. A period of enhanced growth that sped up everything. Things like that. That would make a great unlock after completing the game, and add a lot of variety to replays.
To add a sense of continuity, a very mild rpg element might help. Say, after each mission, the top 5-10 units by stats are selected to go into the next mission. Maybe an enhanced avatar plant, which is 2-5 times more effective than a normal plant, which very very slowly grows and upgrades by time spent playing. Nothing that wouldn't die very easily if thrown at an enemy. Just something to help you feel that it's one continuous campaign, rather than a set of unconnected events. This would have the added benefit of rewarding people addicted to your game, like me.
That's everything I can think of. Thanks for the great game.