Marcus to Kirk pre-warp:
We at Section 31 aren't done with Khan work and have big plans for the rest of his people, now lower your shields.
That would have changed the direction of the film, showing that Marcus' plan for Khan included the attack and was never to kill him. This would then clarify Khan as having motivation to break the bonds Marcus holds on him through his people without otherwise changing the story.
Spock to Khan post torpedo explosions:
Your ship is dead, but your crew is alive and on Enterprise. Surrender and prepare to be boarded.
This would have stopped Khan from going crazy and crashing a ship into SF HQ, killing thousands of people. Given that Spock Prime told Spock about ST2, he had to have told him the source of Khan's biggest rage is the suffering of his people. It could also have been a continuation of Khans "Let play this out... I will walk over your cold, dead corpses" dialog with a line on how Spock can't break bones, but can break Khan's ship.
McCoy to Spock post Khan capture:
Kirk's frozen and we have Khan's blood... but it will take years of research to discover how to bring him back to life.
THAT would have set up a ST3 scenario where Spock, having outwitted Khan in ship to ship and hand to hand combat, assumes command of the enterprise and makes it a point to one day bring back Kirk when it is possible (like the middle of the next movie). This would show this universe won't just destroy worlds, but will make loss personal.
Tyler Perry at the end of the movie:
The "war" with the Klingons has been quiet with nothing but an occasional border skirmish... Starfleet has a fleet on patrol but we are still going to explore the galaxy.
This would give some color to what really happened. We saw a space battle. But it didn't resolve anything on a intergalactic scale: does S31 have a fleet? Is war coming? Was Marcus a lone wolf? This movie seemed like a sci-fi version of SW: episode 2... but without the color of political intrigue.