Personally, I'd think a few clichés to avoid are:
1) The villain does something stupid so the protagonist has no choice but to kill him, in self-defense of defense of an innocent. This relieves the protagonist of responsibility in the kill; and to me makes for a less satisfying ending.
2) The villain realizes all is lost and kills themself. Again, relieves the protagonist of responsibility.
3) Any long-winded explanation from either party.
To me, the best confrontation plays to the characters. The protagonist feels guilty and caused the antagonist. The antagonist agrees and hates the protagonist. The antagonist feels completely justified in killing the protagonist; but the protagonist does NOT feel completely justified; he feels he is responsible for turning his brother into a monster and it is unfair that his failing will now force him to act again against his brother, and actually take the life of his brother after destroying it. The antagonist is all too willing to play on this guilt and goad the protagonist, but somehow the protagonist has to choose to do the one thing he hates most in the world, and compound his own guilt, in order to save innocent lives.
Many final confrontations are too pat. The protagonist dispatches the antagonist with bravado and a clever catch-phrase. No regrets, no angst, no indecision, no emotion but vengeance satisfied. The antagonists have zero saving traits, they are psychopathic evil and care for nobody but themselves, power and money. This makes them easier to kill.
But that is cliché. Still popular, but expected; in most movies the only twist or surprise is in exactly how the beleaguered antagonist manages to trick the antagonist, or pull a rabbit out of the hat to pull off the kill.
If you want to avoid clichés, don't make it emotionally easy for the hero to make the kill, and don't let the villain relieve him of one ounce of responsibility by acting stupidly or rashly. Force the hero to make a deliberate kill he has to think about despite having a clear choice to let the villain escape.