The Clone Wars era is probably going to be different for several reasons, the main one being the relationships between the characters. Some characters (like Rex and Ahsoka) won’t be as close to others (like Padmé and R2-D2) because of the nature of this series.
Padmé’s “supporting cast” will be her family, her handmaidens, her allies, as well as Theon and his allies, so she isn’t really going to be close to any of the Jedi or even the clones.
Cassie will most likely become a Jedi, so she’ll have near constant interactions with characters such as Obi-Wan, Ahsoka, and Rex. That should pretty much balance things out.
I already have a general idea of how “Vengeance” will end. “The Phantom Menace” should pretty much be the next story, unless I can think of another story taking place between them. TPM will take place two years after “Vengeance,” and will be a few months into Padmé’s reign as Queen.
The main issue I have is whether or not to have Theon and Padmé enter a relationship with each other now or wait until AotC as originally planned. It would provide some unique storytelling challenges, and the decade between the end of TPM and the start of AotC would need to be explained, at least in regards to their relationship, if they enter one. I don’t want anything to feel rushed, considering that both of them just met.
Another issue is the storytelling on Tatooine. Anakin, Cassie, and Shmi leaving the planet early would pretty much change everything in TPM onward, or at the very least it would have a monumental effect. It’s too early for Theon, Padmé, the Jedi, and Palpatine to meet them. I’d have to think of drastic rewrites (or cut out Tatooine entirely in TPM and have Theon and company travel to whichever planet that Cassie and the Skywalkers settle on).
Alternatively, the trio could be free of Watto but still have to live on Tatooine as they don’t necessarily have the funds in order to relocate.
Feel free to provide feedback and suggestions!