There are indeed some issues with regard to XI
fitting into canon, even with all the work Abrams and co. have done as far as creating some kind of "plausibility" goes with Spock/Nero coming to "this" timeline from the "original timeline."
I'm not sure how Star Trek: Countdown
fits with either the "original" timeline of the new one, because it's odd how in the comic Nero sees the Shatner-Kirk and recognizes the Pine-Kirk in the film as if the latter were the same.
But in any case, I don't think "Spock Prime" (as he's being called) came from the TNG/DS9/VGR/Nemesis/etc. timeline. He came from a slightly different one, where Pine was the Kirk he knew and the technology existed in the ways that the film displays.
I mean, obviously the technology on the Kelvin
was different from and perhaps more advanced than the technology we might expect from "The Cage" level TOS. The uniforms are different, the ship itself was different.
Which means that Spock Prime, while apparently "our" Spock, was really from a third
timeline, one consistent with the new film up until (and beyond) the point where the Narada
destroys the Kelvin
Does this make sense? Perhaps I'm spending too much time worrying about it and should just enjoy the new film for what it is, a new Star Trek universe that tries not to ignore the old one.