Soooooo... how did it go? The regen revision proposal I mean? Because that essentially leaves two options: If not aproved it's a stomp in Cloud's favor due to AP difference. If it is approved then it would be inconclusive most likely since Cloud can't put Ganondorf down for good and Ganondorf can't really do anything to Cloud.
Though... as @TartaChocholate says, Cloud can add the Death Spell effect to his weapons via the combo he mentioned and turn his swords into holy weapons with Alexander, though with the Elemental Support Materia not the Added Effect. And both effects can be put together if the weapon has enough materia slots. And, IIRC, the Sense skill from the Command Materia does reveal to Cloud the enemy stats and their weaknesses. So it's not unlikely that if Ganondorf restores himself back Cloud would take a look with said skill to know more about what he's facing.
Of course, it depends if the setup is allowed and all that.
Kinda like:
-Cloud: Strife Delivery Service. We brought the evil matter you ordered for your evil plans of great evilness.
-Ganondorf: Ah...at last. You've served me well, but unfortunately your services are no longer needed. And I do not waste time keeping things I have no use for. So, I will be generous and do you a favour *charges dark magic* Any last words?
-Cloud: Not interested.
-Cloud: No hard feel-
- Ganondorf reforms from a pool of liquid metal*
-Cloud: ...Huh...
-Ganondorf: *Evil laugh* Naive fool. Heroes and kings have fallen before me! What could a simple delivery boy do?
-Cloud: ...*Uses sense Materia*
Name: Ganondorf - The King of Evil
Level: Pretty High
Power: Not to be triffled with
Magic: You wouldn't believe it
Evilness: Ohohoho, where do we begin?
Sexyness: Look at dem muscles
Weaknesses: Holy, Death
-Cloud: *Eye Glint* Let's mosey.
Yeah, a sorry attempt to be funny. I apologize =P