FE14 is called IF in Japan, therefore there will be a lot more choices. I am also a fan of an old playstation game called Suikoden, this game features lots of choices which can greatly impact the story. A big goal in that series is to collect 108 'stars of destiny', so every choice you make impacts whether or not you get the perfect ending.
Things from Suikoden that could be in FE:
Choosing whether to fight or flee
Choosing who to give the powerful weapon to
Recruitable characters who can be facilities (eg shops) instead of having useless fighters
Much more complex story
P.S also it would be cool if you had an option of which side to go on, one has say, pegasus riders but no wyvern riders, while the other has wyvern riders but no pegasi. This could be an interesting way of fitting your playstyle.