Any number of temporal incursions could have happened after all the events of pre-2009 Trek and before Spock Prime went back in time, in order to set up any differences that might exist in the Kelvin era versus what existed in the pre-Pike era of the original The Cage.
In fact, I always take Enterprise's NX-01 to be a result of Cochrane's exposure to 24th century time travelers, borg and 1701-E. In this respect it's quite possible that the Kelvin is simply another result of that.
Well, I've argued before that the changes that Nero made would *have* to go both ways - past and future...otherwise the Alternate Universe's past would be full of travelers from a future that wasn't it's own future - and nuKirk could go back in time to say the events of "Assignment: Earth", and hitch a ride with Prime Kirk & Spock back to the Prime universe! (Then again, there's the concept in some sci-fi of visitors from *probably* futures, because the future is in flux - but I don't think that applies here.)
Anyway, so it's possible that changes in the technology in nuTrek were the result of *other* trips to the past, from some time in the Alternate Universe's future (or maybe even it's present) - trips that didn't take place in the Prime Timeline, but do...now...in the Alternate Timeline. (This is also the very same mechanism that would allow for the changes that Nero made to propagate *both* ways in time.)