The final meeting between the hero and his opponent must be more intense than any other battle before, and to be the winner, the hero must risk everything and lose something of inestimable value in order to win. It is not only a physical battle, but an emotional one as well.
The hero's special skill here should make the story stronger, not make the hero invincible. Think of Superman, Kryptonite, and the danger of invincibility to a story. Here's two story final confrontations --
STORY A: Several world leaders are held hostage by Lex Luthor who has tied them to Kryptonite poles. Though weak, Superman manages to rescue them and gets far enough away from the Kryptonite to regain his strength to defeat Luthor.ORSTORY B: Several world leaders are held hostage by Lex Luthor who has tied them to Kryptonite poles. They are surrounded by cameras so the whole world watches.Luthor wants Clark Kent to act as hostage negotiator, and if anyone else including Superman comes near them, an explosion will kill both leaders. Clark approaches but sees the Kryptonite in the poles. If he goes forward and becomes weak, Luthor and the world will know he's Superman. If he backs away, Luthor will kill them immediately.Here's his dilemma -- save two important leaders or lose his identity as Clark Kent.But Clark Kent is more than a role, it's his humanity. Clark belongs to Earth and fellow humans, and he has a relationship with them. They see him as an equal.Superman, however, is a superior alien who can never have an equal relationship with humans who see his powers and are afraid or uncomfortable. If he is no longer Clark, he will be totally alone.Losing his identity as Clark Kent is his greatest emotional fear. What should he do?
Which story is stronger and more interesting? I'm sure you'll say the second one because more than physical danger is involved. Clark/Superman must risk something of great emotional importance to win, and by winning, he will ultimately lose.
To make your story and its ending stronger, find the main character's greatest emotional weakness and hit him there with your plot in the same way as you hit him with his physical weakness.