Damion and I have had several long discussions on the classic history-nerd topic of "which is better, a knight or a samurai?" He knows a lot about the Eastern styles, while I've long been a student of the Western ones. Now, someone who claims to know a great deal about both is taking on the issue. His answer is better informed but essential the same as ours... it depends on far too many factors to make an easy call.
While I can't speak too much to his Asian knowledge, I can say his discussions of Western techniques and technology are bang-on. Like the author, I'm always very surprised that people still think of European knights as crude, brutal, trundling tanks just one unhorsing away from certain death.
The truth was quite the opposite... before the triumph of gunpowder weapons, a knight in plate armor was just about the nastiest thing on the battlefield. They were very well trained and extremely mobile even in full plate armor, horseback or no. Recent tests have shown that even the vaunted English longbow was completely ineffective against them*.
This is not to say samurai are without their own advantages. As I said, and the article relates, it simply means the results of such a hypothetical duel would not be a foregone conclusion. It would instead be, well, very interesting.