Wow! Thanks for putting all of this down.
Different kind of weapons are definitely on my radar of things to add in. You will find some mortars, rail guns and penetrating plasmas, wind to blow projectile back and ion weapons that go through shields as you go throughout the game though. Ido have to work on the game balance to make it less harsh and punishing though, since some player never got around to seeing these things.
I love the idea of population. Having different species could also get interesting and then maybe making them work around in different places could be cool as well.
With regards to the story, I really really wanted to have events in this release, but I ran out of time. The unknown points on the map were supposed to be more of the story aspect and from there add in little story elements to normal locations. I totally agree the story point give players a reason to play, since they would be discovering the story as they went along over different runs.
Speaking of different runs, starting islands would be a cool way to reward the player for progressing in difficulty. Im thinking of trying to get a way to reward the player at the end of a run with an item or block that would get added to every preceding run.
Fuel is something that I have played around with. At first, my idea for fuel was to explore the map. But then I created a linear map where you cannot go downward. This eliminated the need for fuel. So then naturally, I added fuel into the battle. You had fuel tanks that would store fuel and replenish every battle, but this made the game awful and not much fun. So I just removed fuel completely. I also was thinking of ammunition as a resource, but I didn't go through with it. From the sounds of it, it seems like it would be better to have more permanent resources that persist outside the battle.
Thanks so much again for taking the time to write all of this out. I really appreciate it.