Something i notice is that all of the comments on the images are about how things do or don't fit in. One problem with making a game independently is that you know what is there, and what is what. If you don't overcome this thought, you'll never get a visually "perfect" game.
Look at your projects as if you were a critic, what would you do differently? What is really happening? Is it too hard to focus on? What is good about it, and should i continue that?
When someone looks at something for too long, it changes. This change makes what you are looking at more common and natural to you. For people who have not seen it before, this is not what they see.
The pixel work is nice, very retro, and with motion involved would probably be a lot easier to follow.
And one last point, i think that it is the black edges that are trailing the character and enemies off. The black seems as if it were another obstacle, instead of just plain sky. If the point is for them to be in the foreground, then it should be more emphasized, otherwise they seem to attempt to blend themselves into the background.