Okay, I really liked this game. I'll write what I liked about it, and how I feel you can improve. This is a solid game, easily worth 4 stars. I wish more games on this site were as good as this.
Graphics were good, though not quite great. I love 16 bit, but the main character was a little lacking in detail. Still overall they were very good, and nothing to sneer at.
Music was solid as well. None of the background music felt out of place, and I enjoyed it. The music blended in very well with each stage, and I like the option for the sound test. Takes me back.
Controls - The actual controls were fine for me, arrows to move, A, S, etc... I never had a problem picking anything up or moving around the stage. However, I did have some trouble with some of the jumps in the game. I don't if some of the jumps are meant to be very difficult (such as getting high enough to progress), or if that was something that might have been overlooked. I think if the I could have jumped just a hair higher and farther, or had more control over how high I went, it would have been perfect. Otherwise, controls were good.
Alright, onto the meat of the game.
Content was good. Very good. I liked the simple story, but I believe I caught a spelling or grammar error in the intro - I can't check right now without stopping this review. I liked the upgrades, the simple yet dangerous enemies, the stages, the variety in stages, and especially the bosses. You did a really fantastic job making the stages different and making some very good bosses. That is easily the best part of this game. Not to say the rest is bad, it isn't at all, but the bosses were above and beyond in all respects. You did a very good job with them.
Continuing, I liked that after killing a boss I immediately moved forward. It gave each stage a strong sense of continuity that I really liked. That said, I think a health refill should have happened after each boss fight. At one point I beat a boss and had 8 hp. I just killed myself right away rather than try to progress since I knew I'd restart with 100.
About the difficulty, I think for the most part, the difficulty was okay. In terms of how strong each enemy and boss was, and how much damage they did, it was okay. The problem came from certain attacks or hits that were very difficult to avoid. One part in particular was while climbing the tower in stage 2 - I had a lot of trouble avoiding or killing the enemies that shot out of the walls, and at that point the game didn't feel fair. I also had some trouble in the underwater portions with the mines. However, for instance, the "Missile"(?) or spike in stage 2 was fine though, because alarms went off before it shot. So you have the right idea where it needs to be.
Overall, this game was very good, and presents a strong showing in the traditional run and gun genre, and does a great job hearkening back to the 16 bit era. I hope you can either continue it, or make a sequel.
Lastly, I believe I found a bug that is... rather frustrating. I was unable to move left or right and fire the Flamethrower at the same time. That included jumping. I could jump up and down, but not left and right. Given the necessity of jumping and shooting, you can probably understand why this is a bad bug. That's all I found though.