People the timeline has changed, the paradox of changing time of the future from the past was the whole reason of the first movie, so Khan was placed back in stasis and there won't be a problem of Khan taking over the Enterprise as he would have as if everyone remembers, Capt. Kirk and his away team found the Botany bay, and this time they were found by or Used by Section 31, to develope a Starship more powerful than any ship in the Alpha or Delta qudrant. So if you want to change a timeline seriously they can now actually tip the power of the Federation to it's favor over the Romulans, or Klingons which are enemies of that timeline. Further more since now that Khan has helped them develope such a ship or just having designs of it's sort, all future ships could also look far more superior to what the old line of ships could look like, instead of having a Enterprise D, now you can look at maybe a voyage style starship on the new timeline, medicine can have a signifigant change since Capt. Kirk (new timeline) is brought back to life by the use of Khan's blood, so pump a few pints of blood out of Khan he won't miss it, and life is extended maybe undefintely, or no illness, no use for doctors, you never know, Not. Without McCoy the show couldn't work. The movie can go anywhere, new timeline, new things to see...... it will be something to look forward to in 2016.