>>25555016An earlier idea for the story was going to be a take on the Prince and the Pauper. There was also another version (or perhaps it was still the prince and the pauper story) where the emperor meets a llama herder that was going to be much younger than Pacha (and I think he was going to be played by Owen Wilson, but I can't remember). There was also going to be a love interest between the llama herder and some girl he liked, I think.
More details for earlier stories of the script, there was a legend involving the young emperor and somehow being able to ride the sun. Yzma wanted to block out the sun because it was what caused her to age. Her plan was to get rid of the emperor so that he couldn't ride the sun and bring back the light, so that the sky would be forever covered in darkness, and she would look for the solution for eternal youth.
These ideas were eventually altered or dropped entirely for the simpler story we have now. Though the whole "riding the sun" thing is gone, as is Yzma's plot to find a way to stay eternally young you can still see a lot of elements they kept in. Such as Kuzco's crown is the sun. When he goes missing the kingdom is covered in dark clouds and rain. Stuff like that.