i wouldn't mind some exploration on Luna and Celestia's origins.

i still prefer the headcannon that they're physical incarnations of the sun and moon taken shape to act as gods / demi-gods to equestria and to save them from the likes of discord, but given the mentions of them as fillies and the like... it seems unlikely. Plus, now twilight has the tallness and flowing hair of the princesses, so that trait making them unique has kinda been taken away from them... i wonder if this means that Twilight's lifespan really has been extended to over a millennia.

other then that, it's not so much what i would like to see rather then what i'd like changed. Make tings happen more or less then "one thousand years ago". For example i could see Star-swirl, the pillars, and the pony of shadows being an event from two-thousand years ago. the windegos could be three thousand years ago, discord one thousand five-hundred years ago, etc.

it would mean removing Star-swirl from situations like the first hearthswarming, but that could be explained as either being a separate pony with the same title, or a myth that got mixed up in time, like how modern day humans sometimes think of cave-men and dinosaurs in the same era, when they were billions of years apart.