You might want to look at EddieDean’s Clone Wars project; he’s probably done the heavy lifting for you in terms of figuring out how to strip things down to thematically relevant narratives and placing them together.
I actually saw this post and intended to chime in last night before I ran out of time.
If you wanted to do AOTC > [something CW] > ROTS as a self-contained trilogy, you have a lot of options, depending on the story you want to tell. Other Clone Wars editors than myself have created movies from this content, a lot of which are really really strong - so it’s worth checking those for ideas and to see what works.
I guess your key decision is Ahsoka/No Ahsoka/Minimal Ahsoka (maybe where you just explain her away as a temporary padawan or something in the crawl).
If you want to tell simply the strongest emotional journey across the Clone Wars, I think Ahsoka would be your focus. That means going a bit off your brief, and having your Clone Wars episode introduce and develop Ahsoka (hard to do in one movie but probably possible), and then conclude with something that overlaps ROTS and the Siege of Mandalore. I think that’d be the best short telling of the Clone Wars. Your Clone Wars episode might have to be something like Ahsoka’s introduction on Christophsis and perhaps the Cad Bane arc (good romp, develops their relationship, also goes the Palpatine/younglings angle), whilst Obi-Wan is off pursuing Darth Maul in advance of the Siege of Mandalore content, before capping it with Ahsoka’s fall. But Ahsoka’s excellent conclusion really depends on Maul, which naturally would suggest that you include TPM in some way, or at least those scenes, perhaps in flashback.
Anyway, I think that probably isn’t exactly what you’re going for. In terms of a more ‘straight’ AOTC > [custom CW movie] > ROTS, your CW could combine one or more of the following, depending on your priorities:
- If you do go Ahsoka, then the Christophsis content from the movie (and its prequels) introduces her (and has a neat cut where you don’t have to get into the Jabba baby). You could conclude on Ahsoka’s Fall to explain her later absence, though without following it up with the Siege of Mandalore for the emotional gut punch. Ahsoka’s best episodes, which also feature the other main movie characters, which would be easiest to include are Storm Over Ryloth, the Cad Bane arc, the Geonosis arc, and the Onderon arc. (She has better solo episodes but I don’t think you’d want those if you were only going to have her in the one movie - you’d want to keep her tied to Anakin’s story.)
- If you want to highlight the corruption growing in Anakin, then Voyage of Temptation, the Slaves of Kadavo arc, and the Rako Hardeen arc emphasise that. Mortis would add to that if you fancy a big force vision quest.
- If you want to give Obi-Wan some more depth, then you’d be well served by the early Mandalore trilogy, almost all Maul content (though that has the above mentioned issues with Maul), Slaves of Kadavo which nearly breaks him, and Rako Hardeen.
- To emphasise the Palpatine angle and the growing darkness, you have to make a call on whether you expose Palpatine=Sidious in this episode or in ROTS, but I’d suggest the Cad Bane arc, Order 66, and the Yoda arc.
- And if you really want to lean into the Clones, to emphasise the war angle, you’d probably be best served by Domino Squad, Deserter, Umbara, and Order 66. But this would be very light on main characters.
- If you wanted to fill in as much as possible that’s related to other SW media, I’d choose Christophsis (introduces Ahsoka and Ventress), Geonosis (returns to Geonosis, all the main characters, has Ahsoka meet Barriss and then traumatises them both), Citadel (introduces Tarkin, and his relationship with Anakin), Onderon (tests Ahsoka, shows an early rebellion, and introduces Saw Gererra), then Ahsoka’s Fall (return of Tarkin, Ventress, Barriss, and exit of Ahsoka). I don’t know how long it would all run, but this is quite a neat collection that I think would work nicely together.
- And finally, if you just wanted a good romp that gets quite close to cinematic stakes and quality (because bear in mind most of the above content wasn’t designed to be consumed in the way you’re intending here), then I’d recommend the Rako Hardeen arc, for Coruscant, bounty hunters, tension between Obi-Wan and Anakin, all the main characters, and a whole bunch of fun. Preceding that with the Cad Bane arc would give you double Cad Bane, more Coruscant focus, and more Palpatine scheming. Perhaps pop Yoda’s quest in there too.
I notice that all of this is extremely light on Grievous. He might not actually appear in any of those I’ve mentioned. While he does appear in a lot of TCW, a lot of the time he feels neutered. He never even sees Anakin (because of ROTS’ line where he’s suprised about Anakin’s height), so ends up in drawn duels with Obi-Wan a lot, and his military strikes are often defeated. Since originally ROTS introduced him afresh, you could just ignore him in TCW and just let ROTS introduce him as it did originally.
Hope that helps! Ultimately I’m a proponent of the other approach - where I think that the best way to enjoy the clone wars is to keep it as a TV show whilst trimming the fat - but I’m happy to continue helping you think through this if you need someone with TCW loaded firmly into their brain.