I'm still fairly certain that there's nothing to say that it still wouldn't turn out extremely close to the original Star Trek timeline. At the end of this movie, Vulans have already found a suitable planet to recolonize making it very easy for this Vulcan to take the place of Vulcan in later episodes/movies. His mother wouldn't be around in Star Trek IV though... To me, that is the biggest change we would see.
So much will change!!!
For example:
* Pike will likely never end up maimed.
* The Botany Bay will likely never be found now; It's just floating in space. Khan and his people will die quietly, instead of being sent to Ceti Alpha V.
* The encounter with the Tholians is unlikely-- We may see more cooperation with them in the future.
* Vger will not be a challenge now. Spock Prime knows how to deal with it, and will likely advise them to save time.
* Likewise the "whale ship" -- Spock Prime will probably quietly make sure that there are whales on Earth (somehow) prior to its arrival.
* Clearly the Klingons already have cloaking technology-- Years ahead of the prior timeline.
* With fewer Vulcans, other species may become more dominant in the Federation and Starfleet. Andorians, maybe?
* As the mentioned them in the movie, it seems that Cardassians are already involved with the Federation in some way, or at least have made first contact.
* Genesis may never be developed now, as Kirk may never bear a son that grows up to be a brilliant scientist who helps develop it.
* Even if it is developed, Genesis will likely never be stolen and used, as Khan will probably be dead in space by that time.
* Sybok is very likely dead with most other Vulcans, thus the events of Star Trek V won't happen.
* With Spock Prime around, we may see peace brokered with the Romulans this time around.
* Enterprise may not get destroyed as early this time, thus by the era of the Next Generation, that crew may only on Enterprise B or Enterprise C... Or they may end up with Enterprise J by that point.
And so on.