That sounds like a really cool idea, and if implemented well, could make an extraordinary experience.
While it would be a repeat of the FE4 twist, it would be awesome if parallel chapters unlocked as you paired up more people, where in the future you play as their children, where their story would hint at something gone terribly wrong in the past leaving them to pick up the pieces. Done right, it could put the tragedy and ultimate future victory as parallel chapters. You'd have to unlock both to finish the game. To make it even crazier, they could alternate turns during the final chapter. "Player Phase Turn 1", "Player Phase Turn x1" where you play as both armies, in their final battles.
The problem, of course, being to sync the battles up, so that dramatic moments happen "simultaneously". But that's not an unsolvable problem. It would make the final chapter rather scripted, but that's not entirely new for Fire Emblem anyway. Radiant Dawn springs to mind as an obvious boss fight chapter that broke the standard way of playing.
I doubt this game will do that, though, but it could be a fun twist on things.