Complex, fast game engine; weak gameplay.
Problem: Scrounging for ammo is annoying, mostly because you need a lot of it and the easiest enemy to kill (the blade-swingers) is also the most tedious because it takes 3 hits.
Solution: Make the blade-swingers weaker or make ammo more plentiful.
Problem: The special weapons use so much ammo, you're basically penalized for any experimentation at all. What could have been a fun and novel collections of gadgets ends up being one gun and three keys.
Solution: Make the special weapons cost less to fire. Double or even quadrupe the max ammo meter. Don't worry, we'll still want to keep finding extenders for it.
Problem: In theory, the infinite maps mean infinite replayability. In practice, they're just big confusing collections of rooms with no rhyme or reason.
Solution: Use a more advanced map generating algorithym. Many exist online. A mini-map would have done wonders for navigability. And if the different squares on the mini-map lit up as you explored them, it would be an extra incentive, especially if the game kept track of your progress.
Problem: General lack of human interest. Plot, characters, and setting are all extremely bland.
Solution: Add Music! More than one townsperson! Have grandma say things other than "Go," and "Stop." Maybe granny's a tinkerer and you need to take the boss cores to her in order to make a new gun attachment. Maybe the bad guy didn't kill everybody, but kidnapped them for some neferious purpose. Clearing dungeons could mean extra NPCs show up in town, and thank you with powerups. At least the boss talked to you, but even this could have been more made interesting by adding a few twists and turns to the dialogue.
Problem: Combat is BORING.
Solution: Maybe enemies that actually aim at you? And attempt to dodge your attacks somehow?
Problem: Player's tactical options are extremely limited.
Solution: Diagonal movement, the basic attack could slash in an arc instead of just hitting what's directly in front of the player. Combined with enemies that actually track and shoot at you, and a gun with plentiful enough ammo to actually be a formidible weapon, you could have had all kinds of nuaunced realtime combat going on here. You know how, in Halo, there are different "best guns" for different situations? There's no reason you couldn't do something like that, just because it's a 2D game.
Problem: You didn't realize it's not fun. =(
Solution: That hurts. I been there before. I made that terrible witch game. You should have done a nice long beta test on NG Alphas and gotten some feedback while you were still in the early prototype stages. People could have told you stuff to add, and complained about what they didn't like. If you had a deadline, or you were under NDA, then you can disregard this comment. But if you were making this game by yourself, for yourself, there's no excuse for a lack of beta testing! NG,MAG (at the top of this page, on the right side of the orange menu) makes it SO EASY!