All I'm about to say is based on playing only Awakening and Conquest.
Story ideas.
I dont mind Dragon Gods being part of the world but not as the main piece, background stuff. Main plot I would like something akin to Dragon Age Origin at the beginning, were you select a starting point for your Avatar which determines his/her class like Noble, or Thief, etc. Then goes into a Game of Thrones political story. Maybe it can span a generation so that the child system becomes more important. Maybe a Final Fantasy 6 twist where the Baddie wins halfway thru and it's the next Generation that has to raise up to vanish the foe.
Gameplay
Fates with better graphics.
Would like to see supports get exp for all actions not just attacks.
More varieties in support abilities like if you paired a Sage with a fighter the Sage can cast a debuff or buff before the fighter attacks.
Multigrid heals n attacks along with friendly fire.
Add paralogues that become active at A support and must be completed to gain S.
Ability to craft unique weapons.
Dialogue options so we can decide what personality our Avatar has. Maybe even a morality alignment. Tie it into recruitment. Lose or gain units based on your Avatars alignment.
Customizable Avatar child unit.
A full roaming My Castle.
PvP online battles that can have special rules. Like switching on Terrian effects, Squad sizes, etc.