Really well done game. Very complete feeling. I liked the lag in shooting, made for a good level of challenge. Clear theme and storyline. The boss fight was a great level of difficulty.
My one suggestion would be a more progressive level design. I think each level the player should learn or develop one particular skill, and practice and master the skill to be able to complete the level. Then the next level can build on that. It would help the levels feel more varied and engaging.