Yeah entirely agree, the Survivor Series unification match would make the most sense, given that The Rock is going to be there (costing Cena the championship would help put their feud back into play).
I see Del Rio holding on to the briefcase for quite a while, given his enthusiasm to cash in at nearly every opportunity recently, it would serve as a heat building device to have him continually come out and make out that he's going to cash in, only to leave.
If they want to keep Cena strong, the Summerslam match will serve as the rubber match, perhaps it will be for Cena's WWE Championship and Cena will win, albeit in a non decisive manner. Punk would then go over in the unification match (He will still claim to be WWE Champion and the belt that Cena has is a fake manufactured because Punk had the balls to leave as champion) which would feature The Rock costing Cena the championship, but at the same time The Rock would lay out Punk as a "You all forgot about me" angle.