The next Star Trek movie will be released to coincide with the 50th Anniversary, so a certain amount of fan service is to be expected.
I haven't heard any official word on how many of these movies this current team intends to make, but I would guess probably three would be a good number. Hollywood is all about trilogies these days. So I wouldn't be surprised if the next movie is the last of this version. Giving the cast and filmmakers a chance to move on to bigger and better projects.
Using some of the most famous film trilogies as an example. The third film usually heavily calls back the first film. Return of the Jedi had the Rebels attack another Death Star. Spiderman 3 had Spidey going after Uncle Bens Retconned killer. The Dark Knight Rises had the League of Shadows attack Gotham again.
So because of this, Star Trek XIII should take place 3 years into the Enterprises 5 year deep space exploration mission, when war with the Klingons breaks out. The war is especially fast and brutal with the Klingons easily winning every engagement, due to the Klingons having vastly superior weapons. So the Enterprise is sent to find out how the Klingons got so technologically powerful. They discover that after Nero destroyed the Kelvin his ship was captured by Klingons. They studied his ship and reverse engineered the ships weapons and shield technology, and began retrofitting it to their ships.
The Enterprise destroys the Klingon shipyards were their upgraded warships are being built. But not before a massive fleet leaves for Earth. The Enterprise chases after them, and since in this version of Star Trek it only takes a few seconds to travel from Qo'nos to Earth, they get there in a few seconds. But the Klingons quickly overwhelm Starfleet and destroy all of Earths defenses. The Enterprise is badly damaged and all their weapons are destroyed and a few main characters are killed. And thousands of Klingon ships begin carpet bombing Earth, within seconds every major city is destroyed. Big special effects disaster sequence where San Francisco, Paris and London are shown being pulverized by the Klingons Narada enhanced weapons, huge explosions, lots of people getting killed, big Michael Bay style scene. The kind that makes good trailers and gets people into the theatres.
Kirk wants to stay and fight but Spock convinces him to leave as their deaths would serve no logical purpose. So with Earth destroyed the Enterprise limps away (this scene will be an homage to 2009's Star Trek, when the Enterprise leaves Vulcan as it is destroyed)
At some point in the film, either by another expository scene with Old Spock, or some other means, the Enterprise crew discover some type of time travel. Either yet another new method, or a previously used method of time travel. Either way, they realize that with the Earth and Starfleet destroyed the Federation is defeated. The only way to win now is to go back in time and stop the Klingons from getting Neros weapons.
But before they can do whatever it is that will send them back in time the Klingons find them, space battle ensues, more main characters are killed, the Enterprise is destroyed, and only Kirk, Spock and Uhura (because she has clearly replaced McCoy in the Big Three in this version) survive. The Klingons then kill Uhura, Spock sacrifices himself so Kirk can go back in time, which he does, but not before he is gravely wounded. Kirk, bleeding to death is now aboard Neros ship just as it appeared in front of the Kelvin. Kirk fights his way to the Narada's engine room where he sabotages some thing a ma jig, and the ship blows up, before it fires on the Kelvin. It's debris is pulled back into the black hole leaving no trace of Nero or the Narada. On the Kelvins bridge Captain Robau and crew are like "what the hell just happened?" They leave a probe to study the black hole and then continue on their original mission.
"32 years later" appears on the screen we see a fly by of the Enterprise (TOS version with TMP level of hull detail). Interior shot of nuKirk and nuSpock wearing the Where No Man Has Gone Before mustard coloured turtlenecks, playing 3D chess in a shot for shot, line for line, remake of the opening scene from WNMHGB. As they leave for the transporter room the Alexander Courage's Star Trek fan fare plays. Cut to an exterior flyby shot of the Enterprise, "And The Adventure Continues..." (or words to that effect) appears on screen and credits.
That's what the next Star Trek movie should be. Leaving the next team of film makers free to continue, remake or reboot as they wish.