Is it horde favoritism?
Or is it gameplay/gameflow reasons, or
is it entirely a lore thing.. new story.
My bet is on: 2: gameplay/gameflow reasons: Cos Gilneas is right next to a horde controlled territory, there is no alliance quest chains for miles, nor is there an alliance racial capital stronghold.. people were complaining about having to port all over the place in classic for quests, so, they've removed that element, and this puts experiencing Gilneas firmly in the horde and more specifically, Forsaken storyline.
Saying that, there was nothing stopping them from having a level 85 - battle zone, or alliance quest hub that restores the campaign.. but.. I don't think that will ever happen, because the whole idea of setting them up with the night elves is so that they become like the gnomes and trolls are atm, operating from another race.
So they forge a new destiny with new allies. It fits the theme anyway - night elves and not humans, cos humans would be terrified of werewolves, and according to the lore, the alliance humans/dwarves remember WC2, and don't trust Gilneans, so they don't trust their human version, and terrified of their wolf version especially since one mistake can make you end up like a worgen...
The sad thing is though, blizzard has not developed them in Kalimdor with the night elves either, they just plunked 1 tree in Darnassus, and 1 tree in Felwood, and now i claim horde favoritism, because if Worgen were horde, they'd have been integrated much better. I still think Worgen should rebuild on the old Theramore site, and make a new Gilneas, and the night elves also give em some space in Ferelas too.