I think that the best move they could make for a MLP:FiM video game would have to be an RPG or MMO styled game. That way you can customize your pony to the fullest, perhaps import cutie marks, collect gear and items, including specialty items from the show that could be given during events/holidays. The world could be vast and they could even include locations such as the "far away lands" that Zecora is from. Also, you could include many different kinds of competitions, such as racing and flying and even magic duels. You could battle it out and hope the skills you have are high enough to win. You could do training sessions to better yourself if you're into competitive stuff, or go off an quests and adventures. Maybe even run into Daring Do at some point. Bosses would be fairly simple to create as well...Big dragons, a giant Timberwolf, the Hydra, Discord, Chrysalis, Trixie even.
An MMO/RPG style has the best chances in the world of MLP:FiM fans. Not only is there a gaming experience, but you also can connect with fellow bronies and pegasisters who are playing.
As far as the story, doing some form of "Elder Scrolls" opening wouldn't fit since there's only one hero. It could be perhaps a reverse Equestria Girls type of thing where maybe you start as a human who gets turned into a pony and are stuck in the pony world? Then your quest is to find out what brought you into the world and try to find a way to get back...then the story segment could just end with you realizing you like life there. I'm not to sure though ^^"