I'm pretty sure this is a glitch, but it seems that the final boss' bullets shot from the main body don't actually deal any damage.
So for example, if you shoot off the rest of its body, the wings or whatever they are, so that only the main body is left, it's impossible for the final boss to kill you.
A really nice improvement would be changing the secondary shot button to a keyboard button like spacebar, rather than the left mouse button. In those tight, really challenging boss fights, such as the beginning of area 5 bonus 2, releasing the mouse button and clicking it again often causes an unintentional and relatively slight bump of the mouse, which is more than enough to kill you easily because your ship strayed to the side by a few pixels. Also, make the death animation shorter, or skippable. It's quite frustrating going for a challenge like the impossible badge and dying, and then sitting through the 6-second long explosion sequence when all you want to do is jump back into the action and try again.
Perhaps you can disable popup messages while in combat? I got mail in the middle of the tutorial rat fight, and although it didn't make much of a difference, I can see it being a huge problem during more serious fights
So I got destroyed by the Phantom fight in Little Giant Cup due to his discustingly high agility (dodging + attacking so fast I have barely enough time to click my abilities), and just one week later he challenges me to one of the those pathetic rival matches that give alot of money, with all the stats scaled down to pathetic levels as well. Killed him, and unlocked the last character. Is this a glitch?