Not sure how well this fits but probably not deserving of its own topic...
Keep Shulk's route as is, but give him his own boss. Egil outside of Yaldaboath. Sword items appear, Egil will use them and jump around, dodge, and throw laser projectiles. He will also throw swords at you if another one appears that he wants and use the new one.
Too many bosses are big slow things, so I took the mecha away from him and had him outside it for a epic badass sword fight.