I made it through the second half of the 1st season. For better or for worse, I have far less feedback. The last few episodes were simply tighter than the first few.

01x05 - Cloak of Darkness

In the crawl, you mention Ventress’ recent failures. You may want to make it “failure at Kamino” to root it in the immediate context and because I’m not seeing much of a recent track record outside of that. She didn’t really fail in 01x01, though the invasion itself was repelled. I guess you could say that she failed to kill Anakin in 01x00, but again that is kind of an optional part of the series.
This episode might make more sense coming before The 501st. It has a lengthier intro for Ventress and explains why Asoka isn’t with Anakin. Note that if you go this route, you need to remove the whole thing about Ventress’ failure(s) from the opening crawl.
Once again, we have the issue of Ventress knowing and being known by the characters, this time Asoka. She knows that Asoka is Skywalker’s apprentice, and Asoka clearly recognizes Ventress (who in your edit has never encountered her). As before, this could be resolved by slightly trimming the lines/scenes.

01x06 - Children of Night

This episode is very hard to nitpick. It’s long. The part where Savage kills his brother is pretty hard emotionally, but I get that it’s important. I like what this does with fleshing out Ventress and the people of Darth Maul. I also like how it introduces a level of valid distrust between Sidious and Dooku.
I suppose there is once again the issue of how well (or not well) Ventress and ObiWan/Anakin know each other. How do they know her name? The impression that I have of her in this series is that she functions a lot like Maul did in Phantom Menace - a mysterious and clearly dark-side user who appears sometimes and fights with them, then disappears. She should be recognized at this point, but they shouldn’t really know much about her besides her species and affiliation with the Separatists. Some dialogue/scene trims to remove her name from their lines (especially in the early fighter battle) could maintain this status.

01x07 - The Blockade of Ryloth

Should Twi’lek be capitalized in the opening crawl? We generally capitalize nationalities and races today (the British royal family, an African-American singer, the Cuban missile crisis).
Audio-synch issue during rescue of Anakin 29:10 - end. I don’t know if this was somehow an issue with only the file I downloaded and saved, but from the point where Asoka leaves the hanger bay to rescue Anakin through the end of the episode, the audio is off by a few seconds.

01x08 - The Duchess of Mandalore

I have no suggestions. This was excellent.

01x09 - A Strike at the Heart 1

Should Duros be capitalized in the opening crawl? Same issue as Twi’lek in 01x07.
Anakin w Padme at first is awkward, but not inconsistent w Attack of the Clones. They just seem immature/dysfunctional. I understand that we have to have him giving her his lightsaber and that the conversation is the explanation for that. It’s just slightly cringe-worthy.
Why does Cad Bane know Skywalker by sight? Again, are the faces of every Jedi just common knowledge? The dialogue could easily be trimmed in the couple places where he says “Skywalker” to remove the recognition but keep the rest of the interaction intact.

01x10 - A Strike at the Heart 2

The clone bonking his head on a pipe seemed beneath their usual level of competence. Maybe just show them with the night-vision enabled already?
What is the purpose of Asoka’s lesson about the lightsaber at the end? I get that it’s a callback to the Anakin/Padme scene in part 1, and I guess that lightsabers get dropped a few times in all of this, but it seems pretty random. My guess is that in the original version this was a major dialogue thread/lesson. Here it is less so, and this scene just feels vestigial.

Season 1 Final Thoughts:

Overall this is quite good and definitely watchable. The weakest point is the use of recurring villains like Ventress and Grievous. I am not sure how they were or were not built as characters in the vanilla series, but here they hop in and out pretty arbitrarily. That doesn’t really hurt any particular episode, but it does remove their ability to be compelling, especially Ventress (who has what is potentially a really great arc).

In your version we meet Ventress, an unknown dark-side enemy who we see being trained/coerced by Dooku. She lures Anakin away to kill him but fails. This mysterious introduction (actually quite good aside from some of the Dooku parts where it’s hard to see why she is working for him) occurs in an “optional” episode. Therefore, you’d think we would get a proper introduction for her later on. We do, but not until she’s had two more appearances, during which the other characters seem to immediately know who she is, who she works for, even the title (Assassin) that she has been given. She also knows who the good guys are. This is probably because she has fought with them several other times in episodes/content that you cut. The problem is that it feels like that content was cut. It’s like in The Force Awakens when they don’t explain the First Order or the Resistance and then say that you should have read tie-in comic books or novel to understand that. Yes, I guess that can work, but it’s not kind to your audience. Your show is part of a larger universe, but it also should strive to be self-contained, providing viewers with everything they need to make sense of what they are seeing.

In light of all that, I suggest taking a hard look at Ventress in particular and editing, deleting, spacing, or rearranging her appearances to emphasize her arc. I love her initially being an unknown enemy (a lot like Maul in Phantom Menace), but I hate that the good guys get to know her in scenes that I don’t see. I love her big episode on Dathomir, but I wonder if it should come even later in the season, after The Siege of Ryloth or even after the Duchess of Mandalore. Alongside the Mandalorian stuff, it is arguably THE arc of the season.  As for Grievous, he has a far simpler storyline. His big ship gets destroyed and then he leads a fleet against Kamino. Then we see them still looking for him, but he doesn’t show up again. The optional first episode paints him as an anti-Jedi assassin; the rest of the season paints him as a flag officer. I think he’s fine as a flagship officer, but I think that his three mentions/appearances (Malevolence, Cloak of Darkness, and The 501st) should be a more intentional set. This could be done easily by rearranging their order and adjusting the crawl text to emphasize that the hunt for Grievous is a big deal after the Malevolence is destroyed. Maybe (moving it further up in order) to immediately after Kamino, have the Duchess episode start with the line, With General Grievous having escaped again and Kamino being secured, Obi Wan Kenobi and Anakin return to Coruscant to reunite with Asoka Tano and the Jedi Council.

All in all, I see the flow of the season going like this:

01x00 - Dark Force Rising: Mysterious Ventress and intro to Grievous. All else is basically getting the audience up to speed with the Jedi leading clone troops against Separatist droids who are commanded from a distance by Dooku.

01x01 - The New Padawan: Full introductions for ObiWan, Anakin, and Asoka, as well as getting the audience up to speed with the Jedi leading clone troops against Separatist droids.

01x02 - Malevolence: Reintroduces Grievous as a flag officer and builds the threat of the Separatist navy.

01x03 - The Death Watch: Introduces the situation on Mandalore and adds depth to ObiWan. By placing this episode later, we would hijack the reason for Asoka’s absence in Cloak of Darkness and The 501st and use it to also justify her absence here. This would require an adjustment to the opening crawl.

01x04 - Cloak of Darkness: Reintroduces (fully) Ventress while Asoka has her own adventure and ObiWan and Anakin are elsewhere. By placing this episode here, we can juxtapose it with the events of The Death Watch for ObiWan and Anakin, draw out the threat posed by Grievous, and set up The 501st.

01x05 - The 501st: Brings the Ventress threat and the Grievous threat together. This would also close out the hunt for Grievous thread where Asoka has been doing her own thing.

01x06 - The Duchess of Mandalore: Regroups our main characters on Coruscant.

01x07 - The Blockade of Ryloth: Sends our heroes out to the front again.   This one feels very standalone, but it’s a good standalone episode.

01x08 - Children of Night: Brings back Ventress for her big episode, which also introduces Maul (sort of) and sends the season off with a hint of things to come.

01x09/10 - A Strike at the Heart 1 and 2: Again brings the main characters back from the front to Coruscant for the big finale of the season.

These changes would build the appearances of the villains more evenly and do more to justify the way the main characters come and go.