I say at this particular moment it could go either way, to be fairly honest. Judai seems to have his own 'Yami' going for him in that hermaphrodite monster that sometimes takes over and gives him those miscoloured eyes. And he is rather skillful in essence, easilly comparable to the Yugi he's dueling now.
But that's my problem with this; it's supposed to be 'Judai vs the Legendary Duelist'.. Yugi only becomes the Legendary Duelist after he defeats Yami and surpasses him as the King of Games.
This is like saying you've defeated the world's strongest man by going back in time and kicking his ass before he even learned to fight - he's not even the strongest man at the time; kind of an empty victory if you ask me.
The only thing that makes this at least a little bit satisfactory is that Yami will eventually step up to the bat and start working his 'controlling my fate' magic on the deck. But even then.. with Yami still not having recovered all his memories, he still isn't at his absolute strongest.