This looks to be, perhaps, one of the first suggestions since the new release, so let me just say I never got a chance to play the previous version, I was only introduced to Dyson last night (I <3 Indiegames.com ^_^ ). This is a fantastic game! You guys have really made something special. Its like you took some of the really fun components out of SoaSE and made a beautiful new game! Not that I mean to imply you took inspiration from them or anything >_>
Anyways, this is a suggestion thread so on with the suggestions!
A way-point system. I don't mean you should be able to set way-points for a group of seeds, so that they attack asteroid after asteroid (that would seem to defeat the limited moving range in the new version) but if you could set an asteroid to have any newly spawned seeds move to an adjacent asteroid would be interesting. This would help with endgame movement, I think.
While I imagine, and as I've seen suggested by others, you are coming up with more trees to grow on the asteroids, you never know what has and hasn't been thought of:
-shield: despite some of my best efforts, it always happens. The enemy sends in 150 seeds to attack my asteroid that has 400 seeds guarding it. While I know I wont lose it, they still manage to destroy all my trees and take it over for a few moments. Whether or not this could be built at a more expensive cost or perhaps acquired only after certain prerequisites are met (3 out of 4 trees used, or all current trees grown to 75% of their maximum height or something) as I could see building a shield right away as being slightly lopsided.
-Artillery: While having trees that defend my asteroids are nice, perhaps a tree that can attack a nearby asteroid might be neat to try out. They could be used defensively too, aiding nearby asteroids that are being attacked.
-Core defense: have a "root" which protects an asteroid from capture, even if one of the tress is killed and the enemy has access to the core. It could help improve energy regeneration, or kill enemies who make it inside the asteroid
I recall reading something about an editor being put in place, all procedural of course, but I think it would be neat to design custom maps, down to the last detail. It would be fun to design interesting scenarios, say with 2 major choke points, or a player starting with many asteroids while three teamates work to bring him down. That being said, the generated ones do provide excellent replayability!
I know multiplayer has been suggested already, many times, and I'm sure you don't need to hear it again, but just LAN would be fantastic!
I don't know how the game is gonna play out as it progresses, but these are just my thoughts ^_^ Please make the game to be your very own! I really enjoy Dyson so far and I look forward to future developments, so clearly you know what your doing so far!
P.S. A donation, or maybe even a "pre-buy" option (Like Cortex Command or Mount&Blade might be something to look into. I'd be all over that!)