Honestly I think Awakening fucked up Fate's story because of how successful it was. Although I love Awakening, I think it's success made Fates a better game, but Marriage and Children messed up the story. Now I'm okay with Marriage returning; in fact I am all for it and it makes the game better in my opinion. But the Child characters are pointless and totally meaningless to the story (Heres hoping they get some good dlc chapters featuring them).
I think the story does not have to be changed that much. But I think the sibling characters should not have been able to be paired with Kamui, since I think IS wanted to make all the fanboys happy, so they could pair with a sibling but didn't want to stray to close to incest, so they changed the story (Mainly Hoshido) to please them. Now I know Incest never stopped them in the past (FE4), but times have changed.
Speaking of FE4 if they kinda went down that route with how gritty that story was then I think it would have had a better story. Think of it now, lets say in the Hoshido path you end up being over taken by Nohr and losing. With almost all your characters dieing, so then the child characters step in and take over the story and try to take back their kingdom (The story would just be flipped for Nohr). I think that would make the child characters actually useful, and make the story more meaningful. I know it is a direct rip of FE4 but it's not like other FE games ripped off previous games... *cough cough* FE6...