This is even more clear in the earlier drafts of Star Wars. Eventually the "General Vader" from those scripts was combined with the villain Sith Knight Valorum, along with Ralph Mcquarrie thinking he'd need a space helmet to board Leia's ship, and that's pretty much where we got the cinematic Vader.
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Pinhead in Hellraiser was a supporting character. Actually, he is pretty much the Deus Ex Machina who has, what, about 10 minutes of screen time? Kirsty is the main character and Julia was set up to be the series "recurring big bad". Ultimately, Pinhead caught on and he is the only character to appear in all the movies.
Nancy was the hero in ANOES. Nancy passed the torch to Kristen in ANOES 3. Kristen then passed it to Alice in ANOES 4. She remained the "protagonist" for that, part 5, and was going to pop up in the original script for Freddy's Dead (Which would have been 3 movies). Nevertheless, Freddy ultimately became the main character in the franchise.
Charlie the town drunk was a supporting character in Critters. He became more central in Critters 2. He was the only character to show up in the first 4 movies (apart from Terence Mann who was in the first 2, had a cameo in 3 and a supporting cameo role in 4).
I was thinking Nightmare. The series eventually became the Freddy show.
Would the Halloween series fit? The main character in the first 2 was Laurie (even though she was passed out in a hospital for most of 2), and while Michael was the Big Bad, Loomis really only had a small supporting role in the first movie. His role grew larger in Halloween 2, and then he became the protagonist through most of the rest of the movies.
The Saw series. I can't name them off the top but whatever cop or FBI agent that survived a movie will ended up being a lead in a sequel.