So let me just say, as a Trek fan for over 20 years,I can say that I'm a fan of the original Trek cast movies. EVERY TNG movie sucked, and the reboot was different from typical Trek but it was a fun reimagining.
The sequel, needs to add a better overarching story then the first. The story of Nero and his Romulan crew were great but there was no depth -- and make no mistake about it, as a film about the crew coming together, it came together wonderfully and was a great first voyage for the crew. I hear some people say that the next few movies need to show films with nothing too complicated in the plot department. [i]Star Trek[/i], [i]Star Trek: The Final Frontier[/i], [i]Star Trek: The Undiscovered Country[/i], [i]Star Trek: Generations[/i], [i]Star Trek: Insurrection[/i], and of course, [i]Star Trek: Nemesis[/i] were all single adventures really. They didn't tie together to any past storylines; they were just two-three hour long adventures.
Firstly, I know it's controversial, but Benedict Cumberbatch needs to play Khan. Khan is to Kirk what the Joker is to Batman, or what Darth Vader is to Luke. That nemesis, that opponent that trumps you in many ways. They break your rules, or outsmart you, they are not your equal; moreso your worst half.
What I want out of this film, is a Khan who is self-aware. The Khan of the past, with the mind of his future, alternate self. Have Khan be an ally of the Federation, maybe he's found and for some reason is now a somewhat peaceful person. He could be almost like a celebrity. A relic of a lost age. His followers would probably be tied to this as well. Since people are screaming for Klingons, have them be a side villain.
Have him slowly convert back into himself, he remembers Ceti Alpha VI, all of that. Then the Khan of the Abrams series is now mentally fully aware of who he is and what he needs to do. Since this is an alt timeline though, we would again maybe have Khan as an honorary Starfleet officer but eventually have him turn on the Enterprise crew, and Kirk himself. Strand the whole crew on a desolate planet, a reversal of the way Spock stranded Kirk in the 1st film.
Finally, Kirk reasons with a Klingon Warbird. Lies to them or something like that, have them believe that Khan is out for Klingon blood. Then you could see Kirk and the Klingons battle Khan aboard the Enterprise. At the end of the film, leave Khan on a Klingon prison planet.
I could see a self-aware Khan as the best way to have him start out as an ally but slowly have him become capable of understanding what his future may hold for him.
As for people bitching about this being a "Wrath of Khan" remake...
No Genesis Device
Have Carol Markus (Alice Eve); but no son
No themes of old age
No Death of Spock; but I'd love to see a hint -- maybe Khan makes a sly comment