Solid entry! Really good pixel art and sfx. Huge ammount of work been done. But here is some problems I noticed:
1. I think that reputation idea is nice, but it's not quiet working for now? It was hard to me to understand that only red ships attack everyone. But it's nothing i can do about it, just trade with them. And it creates a lot of red resources in your storage but you can't do almost nothing with it (only cure craziness, but it happends rarely).
2. Econmics of the game not seems to work well for me. Espetially violet resource - you can do almost nothing with it.
3. I've didn't get small violet ships at all on the endgame. And I get only one blue and red ships during the game. But it was a whole screen of violet ones instead. You have preseted encounters, you don't randomise them?
4. Turrets also seems to be broken :)
But, effort you put in this game is great, I see how hard it was to make it work. It was fun to play, not looking on problems. It's just a question of pollishing I think. In my opinion, it can be good basis for some bigger game.