One trade-off of the European armor is that it impedes movements making it heavy and clumsy. A clever samurai could make the knight run around to make him exhausted before going for the kill aiming for the critical areas that aren't covered by the armor. Just my opinion.
"What a day for a knight... and a knight for a day!"
I prefer the essays answer too many variables. Besides they never went against each other and there is probably a reason for that. In the end both fighters were the best for what they were meant to be and that is why they never went up against each other. To defeat the other type the knight or samurai would have had to change to meet the need of defeating the other.