I thought that Khan's plan did make sense but he obviosuly got interrupted.
What I was unclear on (and still am) is whether Admiral Marcus knew what was inside the torpedoes and if so why he did bring them onboard the Enterprise. After all, the torpedos would have been kind of useless since they lack a propulsion system of their own.
But then again, his plan seems to have been to strand the Enterprise within Klingon space and cause a war, with the Enterprise (including the evidence of his discovery of the Augments and his collaboration with Khan) being destroyed at the start of the conflict.
It's as good a reason as any to watch the movie again.