Right, I think I’ve finally broken the structure of season three. This took more effort than I expected! The theme is ‘Shades of Grey’, as almost every person compromises or has their perspective challenged, and the third parties grow in power. The secondary plots are Lux (+Ahsoka) and the bringing together of Mandalore and Maul.

Season two, which precedes this, ends with the reveal of the new droid factory. Maul and Savage are at large (playing pirates), Mandalore is safely neutral, but we haven’t seen the Death Watch for a good while.

The episodes we have in season three are:

THE POLITICS OF WAR, where Padmé and Ahsoka meet Lux, and Padmé ‘successfully’ stops the creation of more clones. I think this’ll hit well after the reveal of more droids, but it’s not heavy on the rest of our main cast, unlike the other premieres and finales. I think it should still go first though, because it sets up all of the season’s plots.
THE DEATH OF OBI-WAN KENOBI (Rako Hardeen arc), the way I’ve cut it, is high on Obi-Wan but also gives a lot of time to absolutely all of our main cast, for a huge fun adventure with big stakes and emotions for everyone. It also gets Anakin’s doubt in the council in early. For a long time I thought about making this the premiere, because it’s such a rounded episode, but PoW sets up the season as a whole better.
DISSENT ON UMBARA, is this season’s ‘clone focus’ episode, which I’ve typically put towards the middle. But we’ve just had an ‘everyone’ episode, so we can have one that focuses on others. This’ll also work nicely after Padmé reducing our supply of clones, since Krell’s big thing is throwing away clones. And paced from that by an episode, it allows a little time to have passed in-universe for Krell to get established with that goal (now that he’s actively Separatist). This episode also has a little Anakin and Obi-Wan, so we don’t miss them as much with-
A FRIEND IN NEED, is a great Ahsoka/Lux/Death Watch story, that pushes forward a lot of our main plots. It ends with Lux leaving until the finale, which gives him enough time to get established on Onderon. I may rename this to something like TEMPTATION, since Death Watch are a temptation for Lux, and Lux is a temptation for Ahsoka. Open to ideas here.
PIRATES OF THE OUTER RIM, which features Obi-Wan chasing down Maul (explaining his absence from last episode if you like), and leaves Maul floating in space. I wrestled with putting this earlier to imply that Obi-Wan has been actively pursuing Maul more aggressively, but ultimately that wasn’t enough of a value add compared to other priorities.
HUNTED, starts and ends with Anakin and Ahsoka (but not Obi-Wan, which is neat given the previous episode) and gives us another Ahsoka solo episode. That’s OK, this season is about pushing her on her own. It also lightly reminds us about the success of training the natives on Felucia, which will come into play in the finale.
CITADEL, which I’m reinstating as core, was necessary to include since it gives us everything we’re missing in terms of pacing, at this point in the season. Minor bonus: Echo’s death (even though it’s really throwaway). Major bonus: Since the Rako Hardeen arc shows Anakin’s frustration with the council, we can play that up here as he grows closer to the more imperial Tarkin. I might put some background "Echo"s in the Umbara episode just to imply he’s still part of the squad at that point in time (just not a focal character).
SHADOW COLLECTIVE now has a bit more room to exist since it’s surrounded by two episodes with our main characters while it has none, and finally brings Maul and Mandalore together, ready to kickoff next season. It’s also far enough from Rako Hardeen that we don’t have bounty hunters clashing.
(/10.) REBELS/KINGS OF ONDERON Gives us all our main characters, plus rebellion, plus Saw Gerrera, plus solo Ahsoka, plus Ahsoka learning to let go via the conclusion of the Lux plotline. A worthy finale.

Season four, which follows this, begins with Maul and Death Watch actually taking Mandalore (our first and only season premiere not following a main protagonist).