Here’s something that was brought up on the first page that could work very nicely:

Make Geonosis Tatooine.

This would add heaps to the world of Tatooine instead of just having some random planet we never see again. This is a prequel trilogy that sets up already existing movies, why not do some actual set up? This would explain the anti droid sentiment on the planet, seeing as droids once controlled it.

It would also help Anakin’s character if the bad guys of the trilogy were responsible for his mother’s death. Instead of a Tusken Raider camp, it could be part of the Separatist base? A forward operating base?

Just like the Empire killed Luke’s family, the Separatists would take the last of Anakin’s family.

Maybe this is how Anakin and Padme are captured, replacing the droid factory sequence? They go to save his mom, she dies, and they’re captured, adding insult to injury. This would start Act 3.