I really enjoyed the different paths you can take when building your army - you can build a wall of shields to protect a mass of resource generators and then watch the enemy ship drown in a shower of your own fire power
If I had to give it a slight twist (and maybe you've tried this), I think it would be interesting to see it the other way around (i.e. your ships on the top), and/or maybe make the sprites for your ships appear more "evil" or "alien" and the enemy's ship more "hero". It would make it clearer that you're in control of the villain
Other than that, it's a nice base for a really interesting game, you should consider pushing it further!
sweet stuff!