TWOK hinges on everyone in Starfleet and especially the Enterprise crew being incompetent at their jobs.
Well, it also needs Khan to be the "superior moron" as well.
I figure it's pretty tit for tat.
The "Three dimensional thinking shit gets me everytime. Really, really? That's the big "trick"? Khan never flew in a plane or dealt with submarines when he was a world leader, or for that matter none of his people? Or, how about the chance that mister superior intellect, might browse a book or two on basic Starfleet tactics or Starship operation? How the fuck was he getting anywhere if he couldn't think to command his ship in 3 dimensions? This never came up when he read the Enterprise's tech manuals in Space Seed? "Starshp Navigation for Dummies?" No, never?
And we know he has access to Enterprise design specs: He knew where to blow holes through the refit...the refit that is an "Almost totally new Enterprise" that would have shit in different places from the version Khan is familiar with. And in all the studying the FUCKING PREFIX CODE never came up in his research?
This is why I don't worry about analyzing a Trek movie to much. I'll rip 'em apart if I do.