Their relationship could be portrayed as more of a partnership in the Clone Wars. Instead of just a romantic couple, they could be shown as two people with different skillsets who are equally important in achieving victory. For example, Padme could be more involved in the military strategy discussions with Anakin, using her political knowledge.
Their relationship could be portrayed as more of a friendship at first. They start as comrades in the fight against the Separatists during the Clone Wars, and slowly their feelings develop. This would be a different take from the instant attraction in the movies.
One great fanfiction could be about Anakin and Padme's secret meetings during the Clone Wars. Maybe Anakin is on a dangerous mission, and Padme is worried sick. She uses her political influence to try and get information about his safety. This adds a lot of tension and drama to their relationship, which was already filled with so many challenges in the official story.
One plot idea could be Anakin and Padme having to work together secretly during a Clone Wars mission. Maybe they are on a planet where they need to negotiate with a local leader who is sympathetic to the Separatists. Anakin has to use his Jedi skills and Padme her diplomatic skills to turn the situation around.
One great fanfiction could be about Anakin and Padme's secret meetings during the Clone Wars. Maybe it focuses on how they struggle to keep their relationship hidden while Anakin is constantly on the front lines. Another could be a story where Padme gets involved in a Clone Wars battle in an unexpected way, with Anakin having to protect her and fight at the same time.
Their relationship could be developed differently by having them be more open about their relationship from the start. Instead of hiding it, they could face the consequences together, which would change the whole dynamic with the Jedi Council and the Senate.
There are also some Star Wars fan communities on social media platforms. For example, on Reddit, there are subreddits dedicated to Star Wars fanfiction. You can post a request for Anakin, Padme and Clone Wars fanfictions there, and the community might be able to point you in the right direction. Additionally, some Star Wars fan forums may have sections for fanfiction sharing and discussion.
Another interesting plot could be Padme getting kidnapped during the Clone Wars and Anakin going on a desperate rescue mission. Along the way, he has to face his inner demons and the challenges of the war - like dealing with his Jedi duties and his love for Padme at the same time. This would really test his character and loyalty.
One common theme is the struggle between love and duty. Anakin has his Jedi duties and Padme has her political responsibilities, and their love often conflicts with these. For example, they have to keep their relationship a secret which adds a lot of tension.
As Padme is pregnant, Anakin may start to think more about his future and his place in the galaxy. This could lead to deeper conversations between them about their values and what they want for their family. Their relationship will grow as they both adjust to the idea of becoming parents and all the responsibilities that come with it. They'll have to support each other through the physical and emotional changes that Padme is going through, and also deal with the external threats to their family.
Another interesting aspect in such fanfiction is how their relationship affects the overall Star Wars universe. Their love was a catalyst for many events. Fanfiction writers might explore how their relationship could have influenced the political situation in the galaxy. Maybe they could have united different factions through their love, or their union could have been a symbol of hope for a more unified and peaceful galaxy.