In a special pre-launch group interview, World of Warcraft Production Director Michael Bybee revealed that the team is working on allowing cross-faction instance queues for fully formed groups in a future update to The War Within!
Since the feature was implemented in Patch 9.2.5, only the pre-made group finder allows cross-faction grouping, as players choose who to invite and then zone in together. However, automated LFG like dungeons, timewalking, holiday events, and LFR difficulty raids that automatically invite players to fill groups have remained faction specific. This future update will not change that behavior, except to allow already fully formed groups to queue cross-faction.
I'm actually kind of excited to be able to talk about this one! So first of all, the reason that we have hesitated on this, and some of Ion's thinking that he explained then and is still true today is that we really feel like if you're a player who is super pro-Horde or pro-Alliance and that's what you identify as… you don't want to find yourself queued up with a bunch of random Alliance people that you didn't sign up for.
What we're talking about now is trying to find a way to make it so that people who are in a full group can queue up as a group. They've already opted into that cross-faction behavior and then they can then play in a cross-faction group as long as they're queued up as a full group. That's what we're talking about. It's not gonna be in the initial launch, but we're talking about that being something potentially post-launch, hopefully soon, and I'm super jazzed about it.