The Separatists are in need of a Fleet Commander.
General Greivous with either the Malevolence or the Invisible Hand as Command Ships would be an obvious choice. However Count Dooku could equally be the Fleet Commander of either ship.
However both of them could have their own attack ships, Count Dooku's being his Geonosian Fighter and Greivous in his ship the Soulless One, while Admiral Trench could be added into the game to act as the Separatist Fleet Commander with his ship the Invincible. This approach would make the Separatist faction more viable in Ship battles.
A few extra Separatist ships could be unmanned Droid ships such as the Vulture Droids, the Hyena Bombers, and the Droid Tri-fighter.
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Doesn't mean they'll ever implement them but I also see Separatists getting a faction update soon just so they have some viable synergy for dark side tb.