So like, FFXII where Cid is a good guy and maybe Venat instead corrupts Balthier instead? Or better yet - Ashe. And the plot would start after she annihilates the Archadian empire and you have to stop here.

Or FFXIII where Oerba is the current reality, while everything on Cocoon is from the past, making Fang and Vanille the main party, while the rest take over their original role?

Though the coolest by far I think would be an AU for FFVIII where nobody forgets anything through GF use, so they all remember the orphanage. Think about it - they all know each other through and through, they're happy to see each other again, they have all these memories together, adding to their banter and chemistry. And then the while Edea thing would play out completely different