Meh I think Dooku will get his private ship, bringing both separatist and sith synergy. As for the capital ship, I think it's unlikely we'll get Nute's doughnut ship as it would be hard to fit in. My money is on either Invisible hand or Malevolence, hopefully with the good general as the crew seeing as I already have him at g12+4. Still it's quite possible that the new capital ship will be crewed by Nute or some other unreleased character. Kalani maybe? Would be great.
Seems only thing one can take for granted at this point is that it will be a separatist capital ship. Time to pick up the bug farm again I guess.