In [Into Darkness] they set out finally where the original series started. The first two films – especially the 2009 [Star Trek] – was an origin story. It was about them coming together. So they weren’t the characters they were in the original series. They were growing into them and that continues on in the second movie. So in this movie they are closer than they are to the original series characters that you have ever seen. They have set off on their five-year mission. So their adventure is going to be in deep space.So there's at least one difference identified: in this timeline the crew has grown closer more quickly. Which would go a long way toward explaining how Kirk and Spock have become closer friends in STID than they had during that same period of time in the original series.
But, will we see any familiar bad guys?
The Horta is actually the villain in the next oneReally?
– no – they are in deep space now, so lets see what’s out there.Awwww.....maybe we'll get a Horta crew member, like in the Paperback book series?
Source: Badass Digest