Original 3 Protagonist vs. Final Villains of each series

[Super Saiyan Overlord1007]

Yugi vs. Darkness/Nightshroud (True Form) if you haven't seen that version of him than just use the version of him that used Atticus as a vessel.

Jaden vs. Z-One

Yusei vs. Yami Bakura (A composite of his Dawn of the Duel and Battle City self)

 

[Epicnessbeyond]

Yugi annhilates Darkness
Z-One Annhilates Jaden
Yusei beats Bakura.

 

[Super Saiyan Overlord1007]

Agreed I think myself Yugi will beat Nightshroud. If Atticus is his vessel he wouldn't have too much difficulties given his luck of the draw and broken cards. However against True Form Nightshroud I can see him having some issues. Nightshroud I'd definitely say is the mandatory "Broken Villain" of the GX series. I can see him winning with some difficulties with the God cards he purges him from existence.

Jaden ain't beating Z-One. I can see Yusei on his own competing with Yugi and beating Jaden but Yusei needed the other 5 Signer Dragons and one of the few plot haxes he's ever had to use to beat Z-One. Even with Yubel or Divine Neos I can't see him beating Z-One. I can Yugi struggling with Z-One pretty badly even with the God Cards.

I want to say Yusei stomps Bakura but I'm not sure if I can call their duel a stomp. I'm more than positive Yusei will win but I'm not sure if I can it'll be a stomp out. Even Yugi has issues with beating Bakura.