This game is great. I really liked all the work that you put into the dialogue, nice job. Story's nice, not too cliche either, and multiple endings add to the end (especially the hard ending, good incentives lol). Only thing about this game I would say could use significant improvement (if you ever did make a sequel) is that the actual stages get rather repetitive. Same enemies (literally, same bosses 2-3 times), same firing patterns, same music,... etc. But these are meant to be constructive criticisms. That said, nice job :).
Ok, the game was amazing except for having a lack of weapons for the last boss. I'm sorry, but there is NO way I'm going to spend an hour and a half trying to beat the last boss by slapping him with a rifle.