A better version of the prequels would have clearly established a couple of things: 1. Palpatine’s influence over the separatists is not absolute, and they are open to peaceful negotiations, 2. At least somebody (like Padme) is clearly critical and opposed to the Republic’s militarization and the use of clones from the start, 3. The Jedi are not ontologically good, and/or have significant disagreements with the Republic, the war, and the use of clones.

The clone wars show kinda fixed that. The separatist are more plural and some doesn't agree with Dooku and want peace talks with the Republic, there's a group inside the senate that's do not agree with Palpatine, Padme debate things with Anakin, who always sides with Palpatine and the Jedis are not the paragons of good for most of the galatic people.