Binding Blade: Make Bern a bit more relentless instead of basically gradually buckling down to the Allies after Chapter 16. Particularly Narcian would be somewhat more competent. In Chapter 3, the entire Bern army would crush both Hector's and Roy's army, while Roy and his team had to flee and hide from there on. Eric and the traitors would also pick on Roy until Chapter 8, and Narcian and Co ended up cornering Roy at Ostia in Chapter 8. The end of Chapter 8-15 would remain as they originally were. Then Narcian would flee after the liberating Aquleia in Chapter 16, seemingly out of cowardice, when in reality, that was a feint, and he unleashed an arsenal of powerful dragons against the city, razing it as much as he could to deny resources to the enemy, (not unlike what von Cholitz was ordered to do against Paris in WWII) while Roy and Co have to desparately defend the city to survive. Despite Murdock and Brenya's displeasure at what they see as Narcian's incompetence (for Chapter 13-16) and bloodthirst (this version's Chapter 17), Zephyr allows this to happen because, as per the original story, he was intending to hand over the land to the dragons. Unfortunately, this plan gradually unravels as gradually more people back at home finds out and starts to get appalled. By the time Roy reaches Bern proper in Chapter 21-22, the whole empire implodes into civil war as the rebels supporting Guinevere fighting against those supporting Zephyr...
In fact, this is what I am thinking of doing when I would finally start writing my Binding Blade/Pokémon XY fanfic sometime in the not-so-near future. (PM me if you want to know more.)
Sacred Stones: A more equal division between Eirika and Ephraim's army with you taking control of both, and also have Ephraim his moments of screwing up due to his reckless behaviour. Innes would also have his own problems due to his hostile behaviour -> diplomatic failure/lost opportunity for alliance.
Shadow Dragon: A further expansion of why Medeus wants revenge for his species being percecuted. Also, more characters should join in the conversation besides Marth, and Malledus. I wouldn't mind a subplot with Marth x Caeda running through the whole arc. If Caeda is killed in battle, then Marth would have moments of grief.
Awakening: Oh for the love of everything good and holy, don't make the countries so one-sided for starters, and have better details in the world-building for seconds.
Fates: Make Hoshido starting off the smaller and weaker country, yet gradually becoming more ambitious, evil, and hell-bent on world domination as it grows its strength. And make Nohr as the invading country in the main game, but unwilling and only in it as a last-ditch attempt in self-defense. No, wait, that's my WWII propaganda LP version of Conquest.
Fates (a more serious answer): Remove Valla completely, and make Garon a well-intentioned extremist who attacked Hoshido out of desperation of his starving people, while Hoshido have you deal with some rotten noble people playing isolationist politics and status inequality in addition to repelling the Nohrian invasion.