Obviously, Willy Wonka himself is a must - include. He's the heart and soul of the factory. Charlie Bucket is also great as he represents the pure - hearted visitor. The Oompa - Loompas add a lot of fun and mystery with their strange songs and unique appearance. Veruca Salt can bring in some drama as she was the spoiled brat in the original story.
One idea could be a fanfic where Charlie Bucket discovers a long - lost recipe of Willy Wonka that leads to a new kind of magical candy. Another could be about the Oompa - Loompas' backstory before they came to work in the factory. Maybe a fanfic where a new character enters the factory and has a unique adventure, like finding a secret room full of candies that can grant wishes.
Whether Wonka is an origin story really depends. If the narrative details how Wonka developed his skills, personality, and motivations from the start, then yes. But if it jumps in later in his life, then probably not.
Another possibility is a crossover with 'The Chronicles of Narnia'. The children from Narnia could enter the chocolate factory. They might be amazed by the talking candies and the different rooms. And perhaps Willy Wonka could create a special chocolate that has the power to transport you to Narnia, creating a connection between the two magical worlds.
A jealous former employee of Willy Wonka could be the main antagonist. This person was fired from the factory for trying to steal Wonka's secrets. Now, they want revenge and will stop at nothing to take over the factory and ruin Wonka's reputation. They might try to frame Charlie for stealing candies or causing chaos in the factory.
In a crossover with 'Peter Pan', Peter himself would be a great addition. He could fly around the chocolate factory, causing mischief among the Oompa - Loompas. Wendy could also be there, and she might befriend Charlie and help him understand some of the more complex parts of the factory. Tinker Bell could add some magic sparkles to the already magical environment.
They could start by having deep conversations about the meaning of chocolate and the joy it brings to people. This would help them bond on a more emotional level.