PredakingCrush: taking away the damage done each time the super attack connected would mean he would take even longer to die and my wrist would have wound up even more destroyed, lol
I may be completely wrong, but based on my final boss battle, I believe:
[BOSS BATTLE SPOILERS!]
(1) The game is designed to make you quick-dodge when the boss appears overhead. While you can technically pull off a supercharge or use the gun, it's only barely possible, while doing a quick-dodge gives you a lot of time to attack him correctly.
(2) The boss has no health bar - during this sequence, what matters is
how many times in a row you can hit it. If the boss hits you, the sequence starts again.
Combining (1) and (2) above: trying to pull off the supercharges or using the wristgun is a bad idea. It will usually result in the occasional mistake, meaning that you get hit, and undoing all of the progress you made during that part of the battle.
I had to chow down a few k-bups before I figured out the pattern, but once you do, it's actually a much easier battle than most people think it is.
EDIT: For anyone still having trouble, I seem to recall reading another tip somewhere else. This tip suggested that the boss has a fixed attack pattern that you can memorize (e.g. in front, behind, left, right, above, etc.). I never noticed it during my boss battle, so I can't confirm whether it's true.