A third option would just be to create a new cast/a new adventures. The Universe is a big place and they don't have to run into Sora and Xehanort right away.
Which is prudent because Xehanort is the harder problem to fix. A lot of his retcons take away more than it adds. Plus you can't fix 3 without tackling the games before. So avoiding him altogether is the best option.
The nobodies don't get confusing till Roxas enters the picture. Roxas, Namine, Xion and Vanitas don't give insight into their hosts. But that's a characterization issue other franchises manage better.
Unlike Xehanort, you could fix the nobody concept by just creating new ones. Adaptations could work like second drafts so just learn from 2's mistakes. Which is a theme you can explore in a story by having the new Org learn from Xehanort's mistakes.
Plus if it fails you can write it out easier.