One single thing to fix the story?
I reoriginate the planet. Let’s just start this over and try again.
But if multiple things, I would wind down the Sylvanas arc by feeding her directly to Tyrande. I build up peace between the factions and have the players go on a faction-war-free Mists of Pandaria-Battle For Azeroth style adventure with discovering new lands, exploration, puzzles. There would be still be border disputes and personal grudges but those operate outside of the factions. The big name NPCs are busy working on negotiations and actually leading their people, while smaller, newer NPC leaders step into the player’s role of Commander.