Warning: Spoilers ahead for Star Wars: The Bad Batch episode 12, "Rescue of Ryloth"
Star Wars series, the transitional era between the fall of the Republic and the Empire's rise has lead to some fairly interesting reveals about the Imperial machine and how it was formed to subjugate the galaxy. While the issue of cost was already brought up as a reason why enlisted stormtroopers were favored over created clones, a far more dynamic reason has just been revealed: the clones began to rebel.
In Star Wars: The Bad Batch episode 12, "Rescue of Ryloth," it's revealed that the Empire's occupation of Ryloth went into full effect at the Clone Wars' end. Naturally, this led to frustrations from the Twi'lek citizens who wanted the Republic-turned-Empire off their planet like the Republic promised it would after helping Ryloth fight off the Empire Separatists' occupation. However, rising tensions and escalations from Cham Syndulla and his freedom fighters lead to the Empire tightening its grip. Not only did the Empire arrest Cham and his wife, but they also assassinated Senator Orn Free Taa, blaming the murder on Syndulla himself in order to negate his influence over the people.
However, the lies and the oppression soon became too much for Clone Captain Howzer, as he had served and fought with the people of Ryloth for years. When Cham's daughter Hera arrived with Clone Force 99 to attack the Imperials and stage a rescue mission, Howzer could no longer stand by and follow orders he knew were wrong. After he helped free the Syndullas from their imprisonment, he chose to stay behind in an effort to convince his men what he had come to realize. Remarkably, his appeal struck a chord with a handful of the clones, and they laid down their arms as well, proving that the clones are soldiers with honor at their core beyond their programming and behavior modification chips. As such, it's an ideal that clashes with the Empire's need for forces to obey orders without question (no matter how cruel or dark).
It now makes more sense as to why the Empire chose to create stormtroopers over the clone troopers beyond the simple issue of cost (this is the same Empire that built two Death Stars, after all). The core problem the Empire had with the clones was their honor and loyalty to the people they had been protecting which trumped the Empire's orders, at least on Ryloth. However, it's not a leap to assume that similar acts of rebellion from clones persisted, making the Empire's decision to enlist the new stormtroopers even easier.
While this isn't to say that there weren't stormtroopers and Imperial agents who defected and came to resist the Empire's orders over time (there were), having average men and women enlisted from across the galaxy were much easier to control, rather than clones who had been bred to be soldiers that are inherently honorable and good. In any case, it's a very dynamic moment in the Star Wars timeline that proves the complexity of the clone troopers after The Clone Wars, with Star Wars: The Bad Batch shining a light on the fact that they didn't just become evil after Order 66 (a directive they had to choice but to obey).
Star Wars: The Bad Batch airs new episodes every Friday on Disney+.
