1) Do more with the ‘heroes on both sides’ conflict. Given that the series is more of an anthology series, it would have been cool if they did an episode, or an arc, where the heroes were Separatists who clearly had good reasons for deciding to succeed from the Republic. While they tried to do that with Senator Bonteri, the point got undermined by Dooku assassinating her and Lux joining with pro-Republic rebels.
Heck, they could have done it in a way that made it clear how Dooku was the Separatists’ Palpatine, or shown that there’s a huge dissonance between the Separatist military and political sphere. As is, though, the show itself provides little in the way of compelling reasons why the Seppies aren’t evil. (Most of that actually comes from works set after the Clone Wars)
2) Maul: Many people who follow me know my love/hate relationship with Maul. While Maul did lead to some pretty good episodes, they should have either a) not had him come back or b) had him die during the show.
3) Better written Padme/Anakin. It came off as a bit inconsistent in the show, with one episode having Padme be the more work oriented one and another with Anakin as more work oriented. Also, the Clovis arc didn’t really jive with the relationship we see in RotS.
4) Mortis. Come on, you could have had a story of representations of the Living and the Unifying Force, with the one balancing them and failing turning out to be a representation of the Jedi Order. It could have been really neat. But no, apparently the Dark Side is the new Living Force, and Jedi are doing things wrong by not balancing not-murder with murder.
(I spent my second viewing of the arc waiting for someone to call Father on his bull)
5) Give Santine some support. I really liked the idea of a planet trying to be Switzerland while dealing with their own internal issues. They could have had Santine point out that Mandalore entering the war would make them a prime battleground based on location, or something to that effect.
Also, the Padme/Santine team up episode was the worst written in the series, and was plot relevant. Come on.