Since the Siege of Orgrimmar, the Alliance and Horde have been more or less at peace. Sure, there are skirmishes around Ashran (though honestly I kind of consider the whole island non-canon, as it has essentially no bearing on the plot of Warlords.) While the cooperation in the Siege worked well and both factions were sick and tired of the fighting (and a lot of the players as well,) that doesn't mean that there aren't still some serious issues that remain between these peoples.
Garrosh's defeat probably means a draw-down of conflict in central Kalimdor. Tyrande agreed to let the Horde keep Azshara in the name of peace (though she expresses doubts that the Horde will be satisfied with it,) and while the Alliance I'm sure would like to find a replacement for Theramore (or rebuild it,) things would logically seem to have calmed down in that area.
But Sylvanas and her Forsaken were always a quasi-independent faction-within-a-faction, and while the Orc/Human rivalry has been given a breather (helped I'm sure by the presence of a non-Orc Warchief, though actually, Trolls have historically been the main rival to humanity) the Gilnean situation is profoundly unresolved.
We know that there will be a battle at the Broken Shore when we first confront the Burning Legion - we see the beginning of this battle in the opening cinematic. In that cinematic, Varian Wrynn and Sylvanas Windrunner fight side-by-side. Sylvanas has always been the most dangerous Horde faction leader to the Alliance (until Garrosh, and they kind of were neck-and-neck.) It's probably not a great idea to trust Sylvanas, and she's the faction leader most likely to lean toward the "evil" side of the alignment chart, but she isn't totally irredeemable (though she might be a bit nuts.)
Giving her the benefit of the doubt (which I know is generous,) it's possible that she is really just there to lead the Horde forces against the Legion in tandem with the Alliance. Even Sylvanas knows that this would be a terrible time to pull some crap, given that the Legion is about as big of an existential threat as the universe has to offer.
If Sylvanas wants peace with the Alliance (and it's not clear that she does, given that she tends to recruit from humans her armies have killed,) she's painted herself into a corner - basically acting in such a way that even if she does totally turn over a new leaf and welcome humans back into her lands to found a New Lordaeron, there's no way anyone would trust her. And many would never forgive her for what she had done.
Enter Genn Greymane.
In World of Warcraft, we're given a pretty sympathetic portrayal of Genn. He's an old man who sets aside old conflicts in order to rescue his people from the Forsaken. He is a king who loses not just his home but also his son and heir. And the killer? Sylvanas.
Genn's portrayal in WoW has generally been one of a sad but resolute man who sacrifices everything for his people. But we should remember that Genn is capable of taking drastic measures to get his way. When the Second War ended, Genn Greymane opposed the internment camps because he thought they were too soft a treatment for the Orcs. Instead, he wanted to see them all slaughtered.
And when he didn't get his way, what did he do? He pulled Gilneas out of the Alliance and built a massive wall to keep the world out - cutting off Lord Darius Crowley's lands in the process, which led to a rebellion and civil war.
This is not to say that Genn is without his positive qualities. But while Varian has been learning tolerance and getting a more enlightened worldview thanks to his son, Genn is a bitter, angry old man.
Oh, and he's a freaking werewolf on top of that, which has got to be bad for his anger management.
I've often argued that if the peace between the Alliance and Horde breaks down, it will have to do with Gilneas. And there is some evidence in the beta files that supports this.
We've been told that the Alliance and Horde are going to be too distracted by each other to really push the fight against the Legion, which is why we're rebuilding these class orders. Setting aside whether that's good for the narrative (frankly, I don't think it would be too crazy for the Legion to be enough of a threat to simply say "the Alliance and Horde are not enough,) we didn't really know if this was going to be the kind of open conflict that started in Wrath or if it was going to be more of the kind of mutual interference or reluctance to cooperate that we've seen in earlier expansions (in Warlords, the two factions were kind of left behind, and there was no reason for the Draenei and Frostwolves to have any problem with each other.)
There seems to be some sort of scenario - when it would take place I have no idea - that involves a battle between Genn Greymane on the Skyfire and Nathanos Blightcaller - Sylvanas' First Ranger - on a ship below. Notably, the Horde version ends with you "battling" Genn Greymane, while the Alliance one has you "defeat" Blightcaller.
This actually wouldn't be the first time that Alliance players killed Nathanos (pre-Cata there was a long quest chain that ended with an outdoor raid quest to kill him in Eastern Plaguelands,) but it seems like he's been canonically alive (as a hunter trainer in Undercity.)
Still, the Horde doesn't really have a reason to start a conflict with the Alliance. While Gilneas is still in contention (going by the Horde quests, the Greymane Wall is really the border between Alliance and Horde control,) it was only ever a strategic objective for Sylvanas. Garrosh wanted a port in Lordaeron, and she went to get it. But Garrosh is dead and the war is over, so while I'm sure Sylvanas wouldn't mind having complete control over the peninsula, it's clearly been back-burnered while this whole endless army of demons is pouring in.
But Genn's stubborn and angry, and you can sure as hell bet that he has not forgotten or forgiven what Sylvanas did to his son.
As hesitant as I am to rekindle the whole Alliance/Horde conflict as a central part of WoW, there are aspects of this that are pretty exciting. The Worgen were never really given a great story after they left Gilneas. They kind of stepped off the boat and became furry Night Elves. The promise and potential of Worgen joining the Alliance was that team blue would finally have a "dark" race - a race of monsters who would make members of the Horde quake in their boots, rather than the other way around. Ultimately this didn't wind up really being the case, because in the Cataclysm Gilneas story, the Forsaken were clearly the real monsters.
But as the violent, vengeful id of the Alliance, I think Genn and the Worgen could be stirring things up. Sure, the timing's pretty unfortunate, but I'm ready to see the Alliance make some bad decisions for a change.