The Faction War only works in the form of a lack of trust between the factions, with a mix of hidden diplomatic talks, and isolationist extremists.
Instead of expanding into each other’s territory, if both sides instead pulled back and put up walls, then the players will be given a mix of factional hoo-rahs within those walls, while also being the only characters who can cross the no-man’s-land and interact with the other faction.
With neither side wanting to be the first to strike, (and thus be seen as the aggressor, instead of the aggrieved) the “war” becomes seeing actions taken against either side as originating from the other.
If the Orcs build a nice fortress, then all of a sudden it’s attacked by Quillboar, then obviously the commander will bellow “How cowardly! The Alliance goaded the Quillboar into testing our defenses, show the pigs no mercy so the Humans know we aren’t to be messed with!” All losses are from the 3rd party trying to get one side to throw the first match to light the drums of kerosene, and the PC goes around trying to put out the little fires before they explode.
Have the PC defend their settlement and thwart the third party and be honored by their faction for it, but also have the cool heads in both factions, send the PC to meet with their counterparts on the other side and keep the peace. The Quillboar acted on their own, and the Alliance isn’t responsible. Make the mission a stealth mission where you have to sneak into the opposite faction’s fortress to deliver the missive to your contact.
The reason why Horde partisans hated BfA, is because it forced us to choose between loyalty to the Horde, or to Anduin. Few who play Horde, do so to be told what to do by Anduin Wrynn. Likewise, I would never expect an invested Alliance player take a single quest from Sylvanas Windrunner. Instead of having us basically choose between our faction and subservience to the other, just have us represent the best of our faction, who won’t resort to outright evil for a pittance of 20 gold and a green helmet.
Like, N’zoth was supposed to be the master of manipulation. The fact that he couldn’t be written to be feeding both sides a thanksgiving helping of paranoia and pride to keep them from cooperating against him is the real shame of BFA. No mass killings, no evil Warchief. You had an Old God whose entire strategy was deception, and honestly I don’t think he lied to anyone except his own servants. The Horde and Alliance were simply written as being so eager to kill one another pointlessly, that he didn’t need to do anything.
Yeah yeah, some will say that my idea isn’t a Faction War, it’s just both factions having their own stories separate from each other instead of working shoulder to shoulder for the good of the planet and—
Well yeah.
Boil it all down and that’s all everyone seems to be dancing around and avoiding directly asking for. Blue wants to build blue bases, and advance blue agendas. Red wants to build red bases, and advance red agendas. So long as a Human Sword doesn’t go into an Orc, and a Orcish Axe doesn’t decapitate any Humans, I’d say job’s done.