She changes it a great deal. For starters, the gender difference can bring in a new type of relationship. Instead of the more traditional male - male rivalry, there could be an element of attraction or different kind of respect. Also, her way of handling the Force and Jedi teachings might be different, which would affect how Vader reacts to her.
One interesting idea could be a female Obi - Wan being a mentor to a younger generation in a different way than the male Obi - Wan. She might use her unique perspective to train Jedi. As for Vader, a fanfiction could explore his relationship with this female Obi - Wan in a more complex way, like they have a grudging respect for each other's skills.
One possible plot could be that Vader, without his suit, is found by Obi - Wan in a hidden location. Obi - Wan, despite their past, decides to help Vader recover. As they interact, they start to understand each other's perspectives better. Maybe they even form an uneasy alliance against a new common enemy in the galaxy.
Their relationship might start with suspicion. Obi - Wan would be cautious as he's seen Vader's evil deeds. But as Vader is suitless and perhaps more 'human' in a sense, Obi - Wan could start to see the Anakin he once knew. This could lead to a slow rebuilding of trust.
One interesting plotline could be a battle that takes place in an alternate universe where Anakin and Obi - Wan have different allegiances from the start. Maybe Anakin is a Sith Lord right from the beginning and Obi - Wan has to face his former apprentice in a more cut - throat battle.
Anakin and Obi - Wan could fit into a Marvel fanfic if they were part of a multiverse - spanning story. The Marvel universe already has concepts like the multiverse. They could be brought in as representatives of a different kind of power (the Force). Anakin's emotional and sometimes unpredictable nature could create interesting dynamics with the more stable Marvel heroes. Obi - Wan could act as a mediator between the two universes, using his knowledge of the Force and his diplomatic abilities to navigate the complex relationships in the Marvel world.
Well, Anakin is often very well - written. His internal conflict between the light and dark side can be explored in great detail. His complex relationship with Obi - Wan, from being a beloved apprentice to a bitter enemy, gives a lot of room for character development. Writers can show his journey from a hopeful Jedi to a conflicted individual on the verge of falling to the dark side.
Well, it could be really chaotic. Maybe Anakin and Obi - Wan would be mistaken for new superhumans in the Marvel universe. Their lightsabers would be seen as some sort of high - tech weapons. They might end up getting involved in the Avengers' battles, either as allies or foes depending on how the story is written. Anakin's power could be compared to that of Scarlet Witch, and Obi - Wan's wisdom might be on par with Doctor Strange's.
There may not be mainstream, widely - publicized fanfictions with Obi - Wan gagged. But some independent writers might have created stories around this concept. It could be that in a story, Obi - Wan is gagged during a diplomatic mission turned hostile. His captors want to silence him to gain an advantage in negotiations. This could lead to a complex plot where his friends have to use their wits and skills to free him and resolve the diplomatic crisis.