I think the biggest problem is designing a entertaining game that isn't really allowed to have enemies. Enemies are such a BIG part of most games that it's hard to even design a game without any. Unless you basically turn it into Stardew Valley or Animal Crossing or Harvest Moon (which would have been a good idea).
Actually, I think fleshing out Shimmerwing's story could make for a good enough new story. Where did this butterfly come from? Are there more of them? You could basically go around the new world map collecting these butterflies to return them to their home. "Return to Flutter Valley" or something. It's light, but I think it'd work as a new story.
Some things they could add in a sequel or DLC, (I'm mostly trying to work within this minigame-heavy format they've chosen):
Being able to play as the other 5 ponies in the main game, not just the minigames. I guess you'd have to make new models for all of them so they could all use the rollerskates, though.
Maybe some concept art to unlock along with all the costumes.
More song options in the dancing rhythm minigame. You could also turn it into a slam-poetry contest in the unicorn village.
Just adding Alphabittle's club could give you access to a bunch of new minigames you could add. We could even actually solve that Rubick's Cube!
A home-decorating function in the Lighthouse, like in Animal Crossing.
A garden you can plant a bunch of flowers in for the looks, or fruits and vegetables you could sell for gems. Or maybe make the Uni-Cycling around town more customizable, with different options to choose from?
Zelda-like puzzles? Or maybe some "ruins" that have puzzles that you have to solve in order to get collectibles.
Zelda or Golden Sun-style world traversal, where you have to use magic to create ice bridges to get across a river. Or fly across a chasm. Or create a plant-bridge?
Maybe a minigame where you have to sell or deliver smoothies to different ponies.
A minigame in the salon fixing up ponies manes?
I feel like there's something you could do with the phones. Maybe different minigames based on old arcade games, which would be phone games? Like Pac-Man, or Galaga. Or Flappy Bird. It would be a way to bring Adventure Ponies 1 and 2 back for a modern audience.
Scouting locations for Pipp to take selfies at? I don't know, I'm struggling to find something for Pipp to do with her social media stuff. Maybe...picking a food for her to take pictures of?
Maybe a minigame where you have to decide when to take pictures of Pipp and which pictures to post on her social media? Like she's trying to hold her pose and she eventually ends up pratfalling, and you can choose to either post a "good" photo of her in the pose she was doing or a "joke" photo of her falling flat on her face, with both getting likes, in the end. Hasbro probably wouldn't approve, but...oh well.
Trying to find ponies to buy Izzy's works of art around town? Izzy really hasn't really make any big, sell-able art projects, but...she COULD.
Or a Izzy's Art Gallery sidequest, where she needs inspiration to fill up a art gallery for a showing? Maybe that's how you unlock concept art. "Fluttershy wasn't a unicorn, Izzy" "I know, but she has unicorn ENERGY, don't you think?"
You could do some friendship-matchmaking. Like one pony wants someone to go with them to a art gallery, and you have to find another NPC who also likes art to go with them? It could be a way to bring together the different tribes, so they get to know each other. Like a earth pony not thinking that a pegasus would like to help her in her garden, or something.
Let Sunny play Cyrano to Primrose on a date with Hitch. Give me my Pony Dating Sim, Hasbro!
