I don't know if you recall Madara once had a conversation with Kisame....Madara said he wants to Sync Sasuke up with Gedou Mazou, but he wants to be able to Control Sasuke.
Here is my Latest Theory on Madara's Plan.
1) Madara Has Sasuke fight Naruto.
2) If Sasuke looses and becomes vulnerable, Madara feeds him to GM with the Black Rods
Now for the Control Part.
I/We have wondered why Madara was so eager to offer Itachi's eyes to Sasuke. My guess is that Itachi's eyes have been somehow booby trapped by Madara. The Upshot is that Sasuke now has EMS, but Madara will be able control Sasuke with Genjutsu because he has done something to Itachi's eyes.