Let's talk about Clone Palpatine and The Tragedy of Darth Vader in Star Wars.

It's important to understand that Star Wars was not conceived as the story of Darth Vader nor were Vader and Anakin the same person right up until 1978, the year after the first movie was released.

The first movie during shooting was "Saga I" of "The Adventures of Luke Starkiller" and Lucas's first draft of ESB was "Episode II". But by 1979, Anakin and Vader were the same person and ESB was shifted to Episode V; Star Wars was reconceived as a 9-episode saga.

What this suggests is The Tragedy of Darth Vader was only ever going to be Episodes I-VI of the saga. By 1994 (when he started writing TPM), Lucas was referring to the 9-episode saga as "the saga of Skywalkers and Jedi Knights", 11 years after resolving Anakin's story in ROTJ.

Even in 1999, McCallum and Spielberg were still referring to it as a 9-episode saga. This is after the Chosen One storyline was in place and I-VI would clearly round out Anakin's story.

And yet, in the middle of this, Lucas was directing Tom Veitch to bring back Palpatine.

Lucas suggested to Veitch that a way for the story to continue after ROTJ would be for Palpatine to return. Veitch suggested that Palpatine could survive as a clone, which Lucas immediately approved.

Veitch: "George Lucas told me personally that he loved it. Some people had a problem with the bringing back of the emperor. But as I have explained elsewhere, we did that under George Lucas' direction."

So, there's the history. This ending was always a possibility.