Itachi has proven that 2 people under a form of Genjutsu can release each other by casting Genjutsu on each other.
Here's the deal: Sasuke can use Tsukyomi. He may not be good at it, but he has the ability to. I know this may be a little far fetched, but couldn't he cast Tsukyomi at the moon as Tobi's is reflected off the moon, thus resulting in Sasuke not being affected? Then, he would be free to do as he pleased.
There IS some reasoning behind this as well. Tobi REALLY wanted Danzo dead. Why? Because he had Shisui's eye. The ONLY eye that could cast a Genjutsu stronger than Tsukyomi. It would have benefitted Tobi to actually GET the eye, but he was content that at least NO ONE could use it against him. With Koto out of the picture, and Itachi dead, who could stop him? Sasuke and Madara. Tobi was confident that there was NO chance that Madara could be Edo Tensei-ed. As far as THAT plan goes, Madara is out of the picture. That leaves Sasuke. Tobi kept Sasuke under his wing and will either use him, or kill him. Either way, Tobi will make sure Sasuke WON'T be able to use Tsukyomi against him.
However, Madara is still here, and Tobi may think he's actually gone since the rest of the Edo's are disappearing. That means, in order for Tobi's plan to be foiled, either Sasuke or Madara will live to fight him. Maybe they'll even all meet at the same time and have a ROFL-stomp fest. I don't have any specific predictions for the final fight (except that Madara needs to die), so this is where my theory ends. What do you think?