We can skip the moral quandaries in the first two conflicts between the Alliance and the Horde as those have been beaten to death with no end in sight by the forums already.
One of the first things Taran Zu does, and I don't think Im alone on this, is go out of his way to make himself sound like an ignorant racist who accuses the Alliance of fighting the Horde because they look different. That is the only possible conclusion he could have arrived at given the ten minutes he had to view the Alliance.
"Oh they are here and they are shooting at those green people, it must be because they are green and no other reason. I shall now hate them and make accusatory remarks based on this alone"
He gets slightly better after the Monastery falls and realizes that he was being a colossal @$$hat, but it seems that he now saw himself as no better than the factions, when he is still WORSE....okay maybe not worse than what the Horde has been doing, but we can blame the Horde writers for that.
Then as you travel across the continent helping out people in the typical WoW manner of Kill X of Y and Gather Z for me, you are always prodded by Pandaren about how being militant is bad and that war is evil.
Yes we know war is one of the worst things to happen to anyone or exist anywhere. You'd have to be some kind of bizarre sociopath to actually find some enjoyment or profit from REAL war (Dont want to give the impression that I think WoW is RL). Not to say that spoils of war isn't a bonus when defeating something that absolutely MUST go, but that is a rare tragedy to come about IRL, also Imperialism is apparently frowned upon go figure. But if you want to get that message across then you have to SHOW how war is terrible, instead of just saying "and that's terrible"
The local Pandaren are beset from all sides by all manner of horrors, from Mogu slavers, Saurok Raiders, the occasional Yaungol invasion, the traditional Mantid invasion, as well as other smaller foes. And one of their chief responses to these problems is to completely ignore it as it kills their friends and family and hope it gets bored and leave them alone, See Jade Witch who abducts children and the parents response is to just shrug and keep drinking. Their Shado-Pan are simply incapable of handling everything that is happening at once, because apparently the Mogu before never decided to launch a massive invasion into Pandalands during any of the previous regularly planned Mantid attacks.
Now it seems the only reason Fear got out is because we landed on the opposite side of the entire continent where we woke up Doubt and then Anger and Despair followed and the Shado-Pan fell to Hate and Violence. But according to the Klaxxi, the previous Empress tried to delay the Mantid invasion because she cared about Mantid life, when in truth she was terrified of dying and didn't want to be replaced at the end of the invasion. So really Fear was going to get one of the Empresses EVENTUALLY.
Really the only reason the Pandaren are still alive is because two military superpowers landed on their shores and began to blow up anything that looked at them funny, much to the Panda's benefit. And all they do is complain about it.
Why are we helping these insufferable houlier-than-thou bearmen? According to new Dev developments the Alliance is in Pandaland to help preserve their culture. The idea that we should celebrate and try to live life to fullest. Which would be fine without the taglines, also having a large standing army and military stockpile is bad and all of our defenses should consist of a few hundred elite troops who can only handle about one big problem at a time while sustaining heavy casualties and be incapable of helping everywhere at once.
The Pandaren idea that having a military is bad but having all these ornate valuables and tons of food everywhere falls apart when the Mantid attack, which causes the Yaungol to attack, then the Mogu see it as a chance to attack, and the Saurok attack because that's what they always do. The Pandaren culture was self-destructive in that they had no backup plan or ability to stop a strong invasion force. Their devotion to ornate structures and vanity was completely ineffective and a waste of time and effort when placed in a battle, might have looked pretty for the first 5 sec before the siege weapons tore it all apart but that's it.
I cant even think of a single Pandaren village outside of the Hidden Valley (which was until recently unpopulated) that isnt on fire, being raided, pillaged, or utterly destroyed by something. There was one Monastery hidden in the mountains in Jade Forest, but considering they did nothing while the villages below were being sacked by Mogu and Forest Tricksters, one has to wonder how long they could ignore these problems until they ran out of food.
Were the Pandaren supposed to be shown as a culture that simply could not survive in a war-happy universe? Because if so then its doing pretty well so far, with the exception that in this regard the Pandaren way of life is not something to bother saving as it would simply collapse on itself if something really nasty like the Burning Legion showed up. At best the Alliance would show up, say "Shut up, you tried it your way and you failed miserably when push came to shove. You dont even have a centralized system of government and we are going to take over for your own good.". Which is better than the Horde's "Shut up and obey or feel free to die screaming".
Were they supposed to be shown as a wise people who could exist without armies and war? Because if that was the intention (and I think on the whole it wasn't this but some dialogue writers with that idea might have slipped the text in occasionally to try and get that message to the players) then the message failed horribly, because if anything it just proved that large armies and overwhelming military force is wonderful and will save us all from whatever bad things come our way.
Once again, lets avoid talking about the starter conflicts in Jade Forest if at all possible. This is about whether or not you felt that Pandaren were a race of annoying holier than thou stereotype wise people whose Aesops fall flat on their face in the Warcraft universe because it simply doesn't work here.