The faction conflict was written in a satisfactory back in Vanilla, Burning Crusade, Wrath of the Lich King, and even up through much of Cataclysm. It was mostly just the Horde and Alliance being world powers that squabbled over stuff like land, resources, political influence, trade routes, old grievances, etc. It tended to be the underlying basis for why there were separate Horde/Alliance storylines in each expansion, up until the later patches, when they’d ally with a neutral organizations to start doing end game dungeons/raids against the BBEG.
It wasn’t until Mists of Pandaria, where they decided that the Warchief was instead going to be a lunatic who turned the Horde into a faceless army of evil mooks against an increasingly innocent and squeaky clean Alliance that things started to get silly. Doubly so when it became necessary for the “good” elements of the Horde to team up with the Alliance to take him down.
The renewed Horde and Alliance tensions in WoD and short lived peace followed by increasing hostilities throughout Legion didn’t get a whole lot of criticism- because the Warchiefs acted like they had some common sense and didn’t start off the expansions by blowing up a city or two.
People were even super hyped for BfA, mostly because of its faction conflict themes. It looked like it was going to focus more on the revamped zone stories, faction politics, and war drama, and lacking a central BBEG with army of zombie/demon/monsters to fight for the fate of the world/universe. A return to classic WoW style storytelling, really.
But we got MoP 2.0, only this time everything’s kicked up to 11 and it ends up again being a battle for the fate of all life, where the “good” elements of the Horde have to team up with the Alliance to take down a Warchief gone mad.
The lesson shouldn’t be, “Don’t do faction conflict,” as faction conflict’s been generally well received. The lesson should be, “Don’t keep doing MoP,” as that storyline was contentious then and even more so when they tried to basically repeat it. You can do a faction conflict without having factions blowing up cities, engaging in race based exterminations, and turning into characters so vile that even their closest allies are disgusted by them. We have plenty of expansions where this has been the case!
If Blizzard can’t continue the faction conflict without retreading MoP every couple of years, then sure, end the faction conflict. But I don’t see that as something to be celebrated. It’s just a sad state of affairs.