Crowning Moment of Heartwarming: The normal ending, where Deuce decides not to make a wish. Later, he comes across a girl that happens to look exactly like Starwish, who was able to grant her own wish to become human as a result of Deuce's decision not to make a wish.
Neferiti's theme fits her perfectly; cold and solemn, but with a hint of tension under the surface.
Ensemble Darkhorse: Ginny. Xdanond didn't know how she'd be received so he disigned her in a way that would make her easy to write out in case of sequel. And yet almost instantly she became fan favourite.
Enjoy the Story, Skip the Game: While gameplay is by no means bad it's generally considered So Okay, It's Average. The story however is considered among the best if not the best in a flash games, so it's not hard to find people who don't really care much about the gameplay part.
Fridge Logic: After Mare gives Deuce her powers in the ending, why can Deuce still manipulate water if Iblis is destroyed?
Game Breaker: The Saw Mine weapon is extremely powerful, goes through enemies and terrain, and hits behind you, but is short ranged. When you combine it with the Long Shot skill, which increases the range of weapons, the Saw Mine becomes a screen-spanning dual-directional high-power shredder of everything.
In the Absolute Zero mission, the terrain is very glitchy and thin: ramming a ship into the terrain long enough inevitably leads to finding a "hole" and allowing you to pass straight through the terrain! Probably a good thing, because the mission is built like a maze.
Game Breaking Bugs: You can also get stuck in those holes, essentially dooming you to restart the mission.
Enemy lasers (the seemingly nigh-unavoidable ones that sweep the length of the screen) are also glitchy, and sometimes your ship can pass through them harmlessly without even seeing the "miss" notice.