You seem to come from the technical side to game design, your post is very detailed in a good way. I like it, but you didn't come here for praise so I get right to my critique.
This sentence is very interesting:
The player(s) would fly around and explore the world, fight enemies, and eventually we would want to add RPG elements like quests/missions/tasks, stories.
This is something that apparently happens in game development, a team is working on a game and very late in the process somebody gets the job of writing a story for it. If you do it like this the story will feel like it just happened to be there and may not even fit. The problem here is that all your game mechanics, your turrets, upgrade system, enemies etc tell a story too. You story would feel disconnected from the game if you aren't careful. The player may not put it's finger on it, but he would say it is bad writing, even if your actual story would be solid.
Which brings me to my next point.
You seem to have the individual pieces pinned down accurately, but I can't see that you have to thought about how these mechanics connect, what impact it has on the player or why he will play your game, what the gamer should get out of it (Exploring, crafting, challenging space fights?). So I would advise you to find out what lies at the core of your game idea and then focus on it. Only add parts that fit to the core, just because games tend to have a quest system in this season, doesn't mean you need one too.