Very cool, all around.
I liked the customizability in the Shop area, and the prices were all very fair. My favorite weapons were the Vulcan, Plasma Thrower and Laser Cannon; I didn't find much use for the Spread shot (it just wastes energy) or the Laser (I like to mow down enemies by strafing, not to snipe them one by one or hope I don't miss) Larger engines and energy sources are essential in the game, and both were implemented just right: engines are key to getting those coins left behind, and you simply can't survive in the later levels without a good weapon that's kept fueled. The shields were also nice, but largely unnecessary in the light of below.
My major beef with the game is how many instant-kill attacks there are. I died so many times on the first boss because he moved so quickly and unpredictably. The worms on Level 2 are also instant kill for anything less than maxed shields and armor.
My other issue is the difficulty in picking up coins. Make them perhaps 6 pixels wider, or redo the "collision" code to make it more real-time. I passed through coins many times when my engine was too fast.
The soundtrack was nifty. You did a good job in choosing engaging music from NG Audio (another plus for effort) Most of the sound effects for the weapons were good, but I got a little irritated at the sounds from the larger Spreadfire, the larger Laser Cannon, and the drones.
Also, the jukebox at the end is awesome. I'm totally rocking out at Flames In The Sky :P