Some fall out from this movie - any or all of deteriorating relationships with the Klingons, re-appearance of the magic blood and some consideration given to the (probable) use of it without Khan's permission, more info on how they decided to refreeze Khan with (probably) no trial, and what the plan on doing with 72 frozen augments.
I'd be pleasantly surprised if any of those issues appeared, other than troubles with Klingons.
Other than that more development of all the secondary characters other than Scotty - Bones and Uhura but also Chekov, Sulu and Carol Marcus. Since we're talking wish fulfillment, I'd like to come up with a good serves-the-character reason for anyone appearing in their underwear
Center the action on a strange new world instead of Earth, with Big Epic Stuff on that world.