I think it is time we got to the root of the topic, why it exists, where it comes from, why it is still happening, and where it can be seen. But before we can do that, I think we need to define what the words really mean, so we can better understand it.
Faction bias, it is a word tossed around quite a bit. But what is faction bias? Faction bias is when one faction is portrayed as more powerful, claiming more victories, territories, having more of a spotlight, and even lore quality. When the Alliance and Horde face one threat as a single entity, there is no faction bias, there is no whining about the topic, nor is it even present in discussion. However, when you toss them toe-to-toe, someone needs to come out on top. Right?
When it comes to faction competition, blizzard puts in a tonne of effort and thought into how to satisfy everyone, for an example, when the Sunreavers were exiled from Dalaran, it could be considered a victory for both factions, though a larger one for the alliance, and a political defeat for the horde, with the silver lining of the Horde gaining the military power of the Sunreavers.
Now, where did faction bias begin, exactly? Faction bias has existed since, ironically, Warcraft 2: Tides of Darkness, when it was introduced that units would have different stats, Orcish Grunts would be more expensive, and more powerful then its human counterpart, while human Footmen would cost less but do less damage, and have a little bit more armor. This could be seen in every Warcraft release until the Burning Crusade came out. Then, it came to lore. Even if you don't care much for Warcraft Lore, you still care about how your faction is doing in the world, it is a psychological thing, heck, I don't even play World of Warcraft anymore and I still care about the Alliance and their military efforts, and how things are going over in Orgrimmar.
Now, where do you see faction bias? Faction bias exists everywhere. Quest Text, NPC Diologue, everything down to the structure of your factions base in Twin Peaks. Faction Bias wasn't as big of a topic was it was until the Cataclysm beta, when blizzard made the effort to redo world questing, that meant re-dividing zones up. Naturally, the Alliance had to lose ground. Blizzard didn't expect faction bias to be such a topic, however, when their quest developers and level-designers were re tuning Azeroth. It made alliance players upset that at every angle, it seemed the Alliance lost, and lost, and lost, even when they weren't facing the Horde, examples being the flooded Wetlands, and Sentinel Hill being burnt to the ground. This is simply a show of quest designing motives, in game design, specifically with MMOs, you give your quest writers settings and feels to go on. I imagine blizzard gave the directive to give the feel of destruction, of cataclysmic, apocolyptic events unfolding before you as azeroth was shaken. while the horde had that feeling of being 'Warborn' needing to be shown, as their new warchief happened to be more aggressive then the last. They saw Orgrimmar militarized, and their borders expanded from soldiers rushing across to claim more land for their people, while the Forsaken recently acquired the Val'kyr as of Cataclysm.
Don't stop reading yet, I'm not saying Cataclysm wasn't a bias expansion, infact, it was largely bias. Though some things were unintended to be bias, some things were simply the fault of writers not cooperating, Mists of Pandaria was an effort to get away from that, but the taste of faction bias was left in the air, thats why it is so heavy now. Theramore was the final nail in the coffin for that. Now, it is all that is on peoples minds when they read patch lore, or the books, they look to see how their faction is doing, the alliance specifically picks it apart, and makes a worst case scenario, its stuck in our heads.
The Horde has now been beaten to a bloody pulp, the theory in the previous paragraph can be seen through this, Alliance are still complaining, and Pandaria is making the Horde into the same thing, scrutinizing every word blizzard types, I don't see it much from them, but its been becoming more popular.
I will provide you an example of when faction-lore-bias came around, look at the burning crusade, if that had just come out today, the alliance players would say, "We got a broken space ship and pacifists, while you got a nation!" Sure, people did it a little back then too, but it was mostly jokingly, nobody cared, nor made arguments like you see these days. Now! Wrath of the Lich King, Sure there was the occasional, "Warsong Hold is bigger!" But it wasn't a huge problem, again, nobody really paid any heed to it. Next, take a look at Cataclysm, Southshore destroyed, any lasting hold in Lordaeron lost, Wetlands made uninhabitable, atleast Menethil Harbor. It was a flurry of losses, and clear superior quality in horde questing. It was funnier, more informative, the Twilight Highlands intro was slick and fun, giving you a show of your badass warchief crushing his enemies, and starting an uprising, then replacing a government, while bringing a new clan of orcs into the Horde. The Alliance felt cheated, we felt like while we fought off an invasion of our half-built fort, you completely rebuilt a city, gained an ally, and to top it off, got some awesome lore with it. Next, look at Pandaria, within the first five minutes, you can see what blizzard was trying to do simply by watching the two introduction cinematics. Garrosh is much more savage and angry, while Varian is righteous and a true leader. Next, you see them exchange blows, with the Horde Airship going down, and the Alliance Gunship remaining Airborn, clearly a thumbs up to the Alliance, a pat on the back saying, "We've got your back this expansion, bro." And it was nice, it made us smile, but alot of us were still scarred by our defeats in Cataclysm, mainly the loss of Theramore. Some people, some how, still believe that theramore was better then Dalaran.
I hope this shed some light on faction bias, The 'whining' is psychological, people don't like feeling defeated.
Now I need some sleep, Good morning!