In Khan, the title character is driven by the need for revenge. He give long speeches about how hes been wronged, he sets traps using Kirks friends, he subsumes logic in the face of his overwhelming need for vengeance. Khan is the driving actor of the film: his wrath and his motivations trigger all the other events. That may not be the most original plot, but it still makes sense. Into Darkness is this crazy hodgepodge of modern commentary (drones are bad), political allegory (secret organizations and conspiracies within Starfleet), fear of loss whose contradictions I talked about above, and Khans desire to get his friends back and to be a terrorist at the Federation. The intersection of these themes made for a crazy clusterf**k where individual motivations and characteristics changed based on the needs of the plot. Thats just bad writing.