I’m not sure how much I’ll include yet, but I’m just thinking about the rough Tartakovsky chronology.

As far as I can tell, there’re three main parts:

The opening salvos of the Clone Wars, up to Anakin being knighted. This fits before Ahsoka is introduced in the Christophsis arc.
The Nelvaan arc, near the end of the war, where Anakin gets a vision of Vader. This is interlaced with the following arc but I think it works better standalone.
The Capture of Palpatine arc, which may be harder to fit into the new canon, I forget. But either way, comes right at the end, around the Siege of Mandalore.

There’s also the scene where it’s implied Luke and Leia are conceived, which is cute enough and not too overt. This belongs about eight to nine months before the end of the clone wars. I think this fits nicely after Ahsoka leaves the Jedi order (since in TCW there has been tension between Anakin and Padme, but the loss of Ahsoka could well force him to seek Padme’s comfort), and before the Clovis arc, where things really start to deteriorate. Since it’s just one brief scene I might make it the capper to the Nelvaan arc, which would fit well here. In that placing, we also get these hints at Anakin’s darkness just as we get the further Order 66 mystery, plus Yoda’s doubts and investigation into the dark side, so I think that works nicely as things escalate.

There’s also the scene where Dooku trains Grievous. Initially it’s set near the end of the clone war, where Sidious then appears and says “let’s go capture Palpatine”, but cutting that I think it works earlier on, during the opening salvos, to establish a bit more of Grievous’ place in the war, and get that threat in up front.