OK, that’s the full series run through and considered whilst holding this project’s goals in mind. My key takeways:

Good God, when the Clone Wars is good, it’s excellent
Good God, when the Clone Wars is bad, it’s horrendous
However there is, definitely, a best path through it which highlights all the best and massively minimises the bad, whilst missing nothing important. Which means, of course, that there’s huge value in a quality focused cut.
Less is more. Many of the episodes are overly padded, especially when the show settled into four-episode arcs, and they’re paced around 22 minutes times four, not 88 minutes. Most should end up punchier in the 45-60 minute range.
Ahsoka is absolutely the heart, with incredible character development, and a range of good relationships.
Rex also has great development - though most of his episodes are in clone heavy arcs, not all of which are consistently great.
Quality is all over, though - let the other characters shine too, when they get a really good episode.
Almost all separatist villains lose their malice through serial failiure, and almost all separatist designs are visually uninteresting.

So here’s the next steps:

Take a little break. I’ve not done anything else with my free time since I made the original post.
Read over this thread and my other notes all myself again, to refresh. (Now is a great time for anyone who’s interested to feel free to think through the notes too, and/or offer up any thoughts to help frame the next stages.)
Review the now-polished list of episodes. Create an initial test chronology - pacing Maul equally, then Mandalore and Ahsoka’s development throughout, then best quality episodes.
Probably do a few focused watches to challenge that. I don’t really need to question the Mauldalore stuff because that’s all staying and it has its order, but I’d like to focus on Ahsoka’s development and make sure I have a solid growth for her that focuses on all her best episodes in the right order. I’d also like to consider Rex/Clones a bit more closely. I need to work out quite how much Rex is a core character, and if so, which arcs and relationships best support his development. Finally, plug in the other bests, and do a little checking of other episodes to make sure they’re worthy or not.
I’ll also use this time to pull together and sort some of the additional assets I’ll need for credits.
Then, get to cutting. I might break from the second rewatch to get at least a pilot episode out to you guys first, so we can discuss that and I can take your refinement notes as I watch. So it’ll be pilot episode first (Cloak/Lair), then onto the priority ones in chronological order. I’ll try to set myself up an editing pipeline where I can churn out the simple aggregate+polish episodes while I’m working on the more technical edits of those that need closer attention.
Once I’m confident I can maintain the momentum, I’ll advertise the weekly watch and start releasing episodes.