The military is already a meritocracy. When you are enlisted, youre first 4 promotions (or essentially, you're first 2 to 4 years of service) are freebies. You get those automatically. After that, when you want to become an NCO you need to pass board exams and have promotion points which are accumulated by displaying proficincy in several areas.
Its the same with being an officer. The first three are freebies. If you dont make Captain(Army, Air Force, Marines) or Lieutenant (Navy, Coast Guard) you must have fucked up so bad that you might as well quit and find another job. Once you hit Major you start competing for slots, which is usualy determined by what positions youve had in the past. If you have proven yourself worthy (usualy by showing competancy in PL, Company CO, and Company XO positions) then you get the job.
Well, most things are at least
partly meritocracies, but winning an open slot based on competency shown in past positions is a far cry from, say, a naval cadet somehow taking control of a carrier group in an emergency and the Navy brass saying, He did a pretty good job, let's let him keep it.
What I was trying to say is that assignments in the new timeline Starfleet are (or at least seem to be based on this movie) based on merit over and above other considerations. Ability matters more than experience or qualifications. If we're dealing with Romulans and you speak Romulan, you're the new Communications officer. If you're seventeen but a genius, you're a bridge officer. If you know how to fight, you're on the strike team. You took over sickbay when the CMO was killed, you're the new CMO.
Even with the destruction of the fleet at Vulcan, I'm sure there are no shortage of qualified command-level officers - ground personnel who want to get back into space, folks who happenbed to be off-world at the time, first officers from the ships that were in the Laurentian system. Lots of Commanders, Lt. Commanders, maybe even a few Captains, who didn't cheat on their Kobayashi Maru, who have years of experience moving up through the ranks and are ready to take the next step.
But they are all passed over for Kirk, because in the topsy-turvey world of NuTrek, through what I see as a combination of reliance on field promotion, merit trumping other considerations, and rank itself not being as important or as stratified as in OldTrek or as in our real military, Kirk has incumbancy: He's served as Captain of the Enterprise, done a good job, so they'll let him keep it, even though there are all those command-level officers waiting for a slot to open up.
Here's something to think about: if XO Kirk had been able to convince Captain Spock to chase down Nero and everything ended with that command structure intact, what would the command assignments have been afterwords? The way I see it, Spock would have remained as Enterprise captain, and Kirk would have retained his field promotion to XO, probably receiving a Lt. Commander rank. Of course, that would be partly at the discretion of the new Captain.