From what I can read, here’s how I would personally split them and why:
DRevan, HK, Badstilla, SiT, SM - keep benefits of full Sith Empire team. Remove SiT and move over to Traya once you have Malak.
Traya, Sion, Nihilus, Thrawn, Nest - your Traya is squishy at g9, hopefully a fast Sion and fast Thrawn will get up taunt and replenish protection. I’d save this team for offense probably considering the lower-geared Traya. Remove Thrawn once you get Malak and move SiT to Traya team, move Thrawn to zEP team.
zEP, Vader, Tie, Tarkin, Shore - the best of what you have left, and still plenty effective on both offense and defense with all the right role-players. Remove Tie and Tarkin once Thrawn becomes available, find another suitable fifth (Wampa, Dooku, Sid etc). Tarkin then becomes another viable empire leader with TFP, RG and two others.
Zaul, Zavage, SA, Dooku, Sid - as you said, an effective cleanup crew that can also punch above their weight class. Sid or Dooku can be replaced by a high-Tenacity tank if you can find other uses for them (I mentioned using them in zEP above, but I actually use Sid on a DoT team and Dooku on my Geo Alpha team, for example).