Into Darkness did a great job setting up the third film and I see no reason to throw that all away by going in another direction. We need a war with the Klingons.
The film can open with a teaser depicting the opening battle of the Federation-Klingon War where a fleet of Klingon cruisers almost effortlessly crushes a StarFleet task force. Cut to Kirk recording a captain's log detailing how relations with the Klingons have broken down and all out war started 6 months ago. The Enterprise has been recalled to Earth and assigned a mission vital to the defense of the Federation. StarFleet revives Khan with the promise of a pardon for him and his crew if he helps Kirk complete the mission.
Throw in some epic fleet battles, an intelligent Klingon general, some cool action scenes, some snarky dialogue between Khan and Kirk, and a romance subplot between Carol Marcus and Bones
. The rest of the movie will write itself.