Rebels + Clone Wars vs. The Empire
Episode 5 hinted that the Separatist droids may ally with the Rebels against the Empire.
I think the finale of Season 3 can be dealt with battles between the Rebels reinforced by the Separatist fleet vs. Thrawn's Empire fleet. We are going to see massive ship-to-ship battle as we did in Revenge of the Sith and Clone Wars series.
This would be a great ending because we are going to have a proper mix between prequels SW and Original SW. What is missing in the Original is in the Prequels, and the vice versa. Filling those gaps in the Rebels would do proper justice for the whole SW franchise.
So here is my scenario
1) The droid general returns with a handful amount of Separatist fleets and join the Rebels.
2) Empowered with such reinforcement and new (actually old) droid army, the Rebels plan for audacious attack against Thrawn's Empire fleet.
3) Thrawn's Fleet vs. Prequels' Separatist fleet + the Rebels
4) The Rebels got squashed, and Thrawn wins a decisive battle
This will do Thrawn a long waited justice after original EU was scrapped by EP.7