Play both sides. It's actually something I have always wanted, Fates does it somewhat. For instance, take Sacred Stones. At certain points in the game, kinda like chapter 5x, you would play a map as Grado. Why? It lets you see both sides. Just like Lyon was (to me) either a Tragic Hero or a Sympathetic Villain, we could see what it's like on the other side, how "your team" is viewed, etc.
It might also be nice if we need the heroes to lose a battle. Suddenly you are put in charge of the Grado/Valmese/Begnion/whathaveyou troops, and route the heroes. Heroes then regroup. It annoys me that we win EVERY SINGLE BATTLE. Even the best Generals lost at least once. So those are my mechanics. I would love alternating chapters/sides until say chapter 20 when the armies join vs a greater evil.
Story Wise... Magvel, 20 years post Sacred Stones. Grado has fallen on hard times- despite the best efforts of heroes the people starve, cities lay in ruin. Recovery from the Earthquake is hampered by the fleeing of people to other regions.Eventually, however, new lands are discovered. The Lands of Valm and Archanea are discovered. Valm, on the recovery, launches an invasion of Magvel.
Out of Story: We know, or at least by the wiki it says, that Jugdral, Archanea, and Valm are all connected. Basically because of Camus iirc and his amnesia. And Valm and Archanea are Definetely in the same world. I would love to see all the worlds really be one- after all Manaketes are all in one. Except Tellius. And Tellius doesn't fit in, imo, only because it has the two Godesses. Despite the Demon King I do feel Magvel would fit in- it has Manaketes, and all the staples.