We know in the Canon timeline that ultimately by the start of the Galactic civil war era the Separatists were on the decline. I love how you have added a lot of content with the introduction of a new series of heroes for their faction. I am curious how you think they fit in as a major faction of the era. If one is to surmise what the separatist's want at this point it is still to overtake the imperial senate and end the ceaseless war with the galactic empire, by replacing it with the Confederacy. This forms the consensus that the CIS is then at this stage as a remnant probably more desperate then even the rebellion. This would then lead to the logic that the CIS would even be willing to go to much more aggressive and insane lengths to attempt to stop the empire. At this point it simply leaves me questioning then what would they have done to attempt to remedy the creation of imperial star destroyers. Then you have to consider how would they deal with the creation of the death star and the executor class dread naughts. The creation of super weapons and larger flagships and modifications of they're own would then have been considered.
The Subjugator class dread naught also known as the Malevolence would then have been an excellent craft to rebuild to attempt to rebuff the creation of the Executor. I have no doubts that a modified later clone war era Lucrehulk eventually could have been designed to have missiles and proton torpedo's along with shields and more quad Turbolaser cannons. So as to the counter the extremely powerful star destroyers they faced by this time period. As an added and desperate touch the Separatists I don't think would have continued on without attempting to find a leader to lead the confederacy from a force perspective. Darth Mauls survival into this era as a metal amalgamation on Tatooine would be a excellent start simply due to his hatred of Kenobi and of the Emperor. As for superweapon's I was thinking along the lines of something more unique but historically something the Separatists tried to use to defeat the Jedi during the clone wars. During the dark reaper crisis the CIS previously attempted to build and reconstruct the dark reaper and it was destroyed on Thule in 20 BBY, during the battle of Thule by Anakin Skywalker.
Then once again the Jedi scattered its remains across the galaxy to attempt to prevent it from being rebuilt ever again. If this was to be an added addition it would be interesting to slowly be able to gather the parts for it as the Separatists to destroy the rebellion and the empire. As a counter to the weapon Vader could be the one to attempt to stop as it was him originally would did defeat it and a rebel hero could also be substituted to stop it as well. These were just some contextual idea's I had I felt mentioning. Feel free to listen to them or disregard them as nonsense. As modifing a mod takes a lot of time and hard work thanks again for this awesome mod. But as the Canon timeline mod I could see how this could cause some rage especially from Imperial lovers and rebel sympathizers alike.