Fluffle Puff
Thought of this while coming up with other ideas. Essentially, an alternate version of S5E09. Fluffle Puff moves to Ponyville and is given a tour of town by Spike. Along the way she sees many pony's everyday lives and struggles, some of which she intervenes in, while others she just finds entertaining.
One specific idea, and the reason I bothered to include this synopsis, is for Fluffle Puff to see a changeling (the one that showed at the wedding in the actual episode) being bullied by ponies. She save it, and gives it enough love to survive. This would show ponies that changelings can feed without harming anyone. The reason for this is that it sets up an epilogue, years later, where ponies and changelings achieve peace, and Chrysalis is introduced to Fluffle Puff during the celebration (Chrysipuff is adorable).
WARNING: if anyone does this story, please ask permission from Fluffle Puff's creator first. I'm not actually sure who that is. I know mixermike622 does a lot of artwork for the ask Fluffle Puff blog, but I don't know if they're the original creator or not.
Ponyville Wonderbolts
This is something I want to include as part of a ~verse story I'm toying with. I still intend to, but it could easily be done in the canon universe.
The Wonderbolts are more than stunt flyers. They are an elite military unit. And Twilight Sparkle, being a princess and having a castle, is in need of some kind of protection, but doesn't want to have royal guards like Celestia or Luna. The result of these two facts is Spitfire moving to town for a while, and training Rainbow Dash, along with several other pegasi, to become the Ponyville division of the Wonderbolts as well as Princess Twilight's personal guard.
The story would consist of training as well as other important issues such as uniforms or initial recruitment. Possible Twidash or Spitdash could occur.