First off, I love this mod so much. It brings everything I wanted to see with the Clone Wars to life. So thank you so much.
For improvements, there are few things that I'd love to see.
#1. Separate the Clone Commanders from the Jedi. This should happen because there were many instances where Obi-Wan went on missions without Cody, etc.
#2. Add a Clone Combat Medic to every Platoon (like you did for Torrent Company). This is how it is in the US Army/US Marine Corps and how it seemed to be in the GAR.
#3. Allow Clone formations to spawn faster from the transports at reinforcement points. The way they currently do so is completely unrealistic. Like an experienced air assault unit like the 212th wouldn't deploy so painfully slow and get cut down by a Droideka while getting in formation.
#4. Add Jedi Master Stass Allie + Commander Neyo and the 91st Reconnaissance Corps.
#5. Re-add the 442nd Siege Battalion, and 187th Legion, they were in the regular Republic at War but were taken out in the sub mod. Same with the 2nd Airborne Company of the 212th. When the 212th spawned in the regular RAW, two of its squads had the different Armor of the 2nd Airborne Company's Clone Paratroopers. It would be really cool if actually dropping in Clone Paratroopers could be done, but if not, then I think that the Clone Paratrooper's skin should at least be re-added to a quarter of the 212th (Phase II) or the 2nd Airborne Company should be made its own unit.
#6. Add the AT-OT walker and allow the AT-TE to carry two squads again. The AT-TEs should also be able to carry at least 9 Troopers instead of 1. The AT-OT would be considerably less armed, but the Troopers inside would be able to shoot still with their own organic weapons. Re-add the AT-AA from FoC as well, to counter the Droid Gunship. Also add the SPHA-T, which would move very slow, but have the longest range of any artillery in the game.
#7. Re-skin the Phase II 41st Elite Legion Troopers to how they looked on Kashyyyk. Also, allow any type of Clone to be recruited with the appropriate armor. For example, while Obi-Wan is in orbit, allow the recruitment of 212th Troopers, 212th Plex Troopers and 212th Medics.
#8 Give Ki-Adi Mundi the self-heal bonus. He was a Jedi Master and on the Jedi High Council, if anyone should have it, he should definitely be one of them.
#9 Add Clone Shadow Troopers. They could go undetected to planets and be able to see the base layout. They could be deployed in battles, but wouldn't really be too powerful. They'd be able to cloak and sensor ping, but their blasters would only do as much damage as a single standard Clone's. The Confederacy could have a similar intelligence gathering unit.
#10. Add Ghost Company of the 212th, like you did for Torrent Company of the 501st Legion, with Waxer (Platoon Leader) and Boil, etc. Like you did for Denal, Echo, Fives, Hardcase, Kix, etc.
#11. Maybe add veterancy points. Like the more battle experience, any unit gets, the more powerful/resilient they become.
#12. Give all Clone Infantry the ability to swim, entrench and take cover. Clone Troopers could definitely swim, and having the ability to create basic fortifications (like dig foxholes) would be realistic. Lastly, I understand why Z-6 Troopers can't, but there's no reason why ARC Troopers and ARF Troopers can't take cover.
I don't think any of these changes would make the Republic anywhere near over strength, but I would totally be fine with the Confederacy being buffed to see these changes in the game. For example, maybe have B1 Battle Droids only cost 25 credits.

THANK YOU SO MUCH for this mod. Sorry that I am not technologically proficient enough to help out. I'm a Soldier myself, so these are just some things that I'd LOVE to see in the game.
Very respectfully, Logan F. Crooks