I vote that red pandas belong to one faction, while the black pandas to another. I firmly believe that if you're not going to have one new race in each faction, there at least needs to be a very notable difference in appearance.
Maybe even a faction specific mount. Something.
This is something we really
don't want to do. There's no genetic separation between the pandaren who choose Horde and those who choose Alliance. We also want to avoid a scenario where, if you want your pandaren to look a certain way, you're pushed to one faction. The whole idea behind adding our first neutral playable race to World of Warcraft is that anyone can create and customize a pandaren, regardless of faction.
It's a race we just didn't want to give to only one faction. And prohibiting customization options in any way based on one's faction choice defeats the philosophy behind our decision to some extent.
We're fairly confident there won't be any significant gameplay complications from this either. There are plenty of ways for players to customize their appearance, silhouette, etc. as it is, that nameplates have been the most trusted method of determining friend from foe for quite some time now.