CLONE CADETS

The cold open was a great suggestion. Starting right into the action makes the episode engaging from the start, for a moment I forgot we hadn’t had any credits yet 😄 And the rest is history. I agree with Wexter regarding the timing of the fade to black.
Good call on adding Fives referring to Echo by name! The new establishing shots before the test fit really nicely and the transition flows great.
I’d say keep the talk between Shaak Ti and Lama Su, if just for the worldbuilding aspect and to give Shaak at least a bit of screentime.
Hevy and 99’s talk worked better than in the preliminary versions. Regarding the transition to Rookies, I’d say it would feel more natural with a couple seconds more of black screen with the “Two weeks later” card before the establishing shot.
On the matter of technical issues, Commander Colt’s second line of dialogue still gets lost among the sound mixing. The first one is corrected though 😃 Also, after Brick says “More like an impossible task”, a very faint line can be heard on the left channel of him saying “You can’t be serious, Eiles”. Is that supposed to be an unpolished part of the edit or is a remnant of a cut exchange? I’m leaning towards the latter.

ROOKIES

I kind of missed Cutup’s death. I know we don’t spend much time with him in this version but, still, it’s a brief scene that also sets up the threat of the Eel (this creature feels somewhat random in its current only appearance without having been established prior to it). Restoring it would also address the continuity error just created where 4 clones are said to have escaped but 3 are shown alive.
Are you still planning on adding a new pre-mortem line for Hevy?

As a minor thing that caught my attention, it’s interesting seeing how the show improved on the visual department over the years. Rex and Cody’s face suddenly look a lot smoothier and more expressive after the transition into “ARC Troopers” footage.

ARC TROOPERS

Fives and Echo suddenly having the blue-striped armor of the 501st is an easily forgivable continuity bug.
A minor thing but maybe you could try keeping Ventress’s line “Keep playing with your droids”. The exchange with Grievous would feel more natural. I like their rivalry and mutual teasing of each other.
The pacing of the battle really benefits from cutting the Obi-Wan swimming bit and the later half of the encounter with Grievous. However, since Obi-Wan now does not appear again after forcing Grievous to retreat, maybe you could cut right before he starts chasing after him.

CONCLUSIONS
All said and done, great work on this, and more importantly, I’d say an improvement over the presentation of the originals. The three episodes blended together are a much comfortable viewing experience and not only because there’s no need to jump between seasons anymore while binge-watching, but because the narrative really benefits from the merging, with each chapter working great as a well differentiated act and ARC Troopers in particular being a strong climax. Also I’d say having the Dominos fail their test at the beginning makes for a more powerful message and growth for Fives and Echo.