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After reading this again, some of the ideas you mentioned, especially about the customizable missions and storyline, I was reminded of Endless Sky, a great open source space-themed game. You might enjoy this, as it even has some of the mission types you mentioned, including escorts and battles where you attempt to destroy an enemy fleet.

Yeah, I played ES a year ago! It's probably gotten a lot of updates since then, but I still like your game's graphic style more  :D