Re: J.J. admits keeping Khan's identity a secret was a mistake
I don't think they really wanted an alternate timeline though. That's just a bone thrown to fans who care too much about that kind of thing. It's pretty obvious that they just wanted to do a reboot, and that's essentially what we're getting.
How do you know what they wanted? All this "bone thrown to fans" stuff is just what certain people insist on believing. It's only "pretty obvious" that people not involved in the production of the films will continue to make this claim despite not having any actual evidence for it. And it's irrelevant anyway, since we did end up with an alternate timeline. In any event, even if they had rebooted the franchise, they would still be able to have the Borg show up earlier.
Whatever happens on earth, that up there, that's the endgame.