TNG's "Parallels" amongest others such as TOS & DSN's Mirror Universe episodes etablished that there were multiple alterante realties/parallel universe use what ever description you like. The new films simply take place in one of those.
Yes but how were we (the audience of ST09) to know if it were a Mirror Universe or a replacement universe that happened in FC or City on the Edge of Forever.
As people have pointed out it doesn't really matter except to the fans as the Abrams films are not likely to deal with the Prime Universe.
It really amazes me that nearly six years later people are still upset about this when Abrams and his team bent over backwards to preserve everything that came before their first film. Mind-boggling.
For what it's worth, my opinion on the matter: it's a new universe created by Nero's shenanigans, that exists alongside all the other parallel and alternate universes and timelines we've seen already. Everything from the "Prime" universe still happened, it's just the timeline has been reset and we're following this universe now.
The greatest surprise/joy in the 2009 film was that Spock Prime wasn't able to restore the timeline and that for once, we (the audience) were going to have to live with it. No easy reset, still preserving what we know happened before, but wiping the storytelling slate clean for new adventures with familiar characters. It could not have been done in a more fan-friendly way.