This is probably the first time I've ever finished a top-down shooter, because they're really not my kind of game. The story in this one sucked me in from the very beginning - I didn't shoot any of the supply ships because I already felt sympathetic. Without ever seeing a single character, I was drawn in and wanted to win for more than just the sake of beating a game. That's a rare quality.
Beyond a really interesting, well developed story, the game also had good mechanics. Even though it was a little frustrating to be slow in the beginning, I still felt like the controls were responsive - there was none of the sliding around that plagues a lot of flash games. I was generally able to remember where the upgrades were located and I was able to prioritize what I needed pretty well. I think you struck a really good balance between being challenging and being fun, because I didn't feel too defeated when I didn't beat a mission on the first try. There was always something else to do until I was upgraded enough to do it, rather than just grinding away on the same stuff (I only had to mine for a couple minutes total).
I really can't suggest any improvements. Great job!