To repeat my mantra : when it comes to "who would win ?", I believe much more in professionnal, organized, efficient and disciplined army than in romantic, personnal and glorious aspect. "Gods of war" Spartans were crushed by "professionnal" Thebans, who were themselves crushed by "even more professionnal and organized" Macedonians. In fact, history has a very strong correlation about how professionnal armies win against other kind of armies, even if they are made of supposedly "bred for war" fighters.
"Discipline > personnal talent" when it comes to the battlefield.

I may concede that the typical samurai would win more often than not against the typical roman legionnary (though I'm pretty sure he would have a very nasty surprise when it comes to fighting someone skilled with a shield), but it's because the training and martial arts of the samurai was oriented that way, while the typical legionnary had his training geared more about being a "soldier" than a "warrior" (that is, practice with moving in formation, keeping ranks, obeying orders, fighting as a team, etc.). And this is THIS training which is by far the most efficient in war.

Also, I'm convinced that the overall organization of the Romans was FAR superior to the overall organization of the japanese armies, and allowed for much better and more sturdy strategical planning and resilience.