Earlier today I posted a blog with some of my old ideas (totally not shameless plug). Here's one that's basically copy+pasted, free for anyone to use if they so choose:
RD and FS Highschool story:
I'll start with this one as the recent episode preview revealed characters which would make this story contradict canon. Fluttershy, an only child lives mostly alone at her home atop a large hill. Her parents are amateur stunt/speed fliers, (think a step below the wonderbolts). Their jobs has given them enough financial security to allow them to support Fluttershy's wishes of having a home near the ground and have her attend Cloudsdale High. Unfortunately, because of their jobs, she hardly ever sees them. A big character point would be that Fluttershy's lack of confidence is due to the fact that her parents are really good at flying, yet never took the time to train her.
Rainbow Dash on the other hand would live with her single dad. Her mom passed away giving birth to her. Her 'dad' seen in the show would be her uncle (who RD loves and would be in several scenes), while her real dad would lack the features that RD inherited from her mother (rainbow mane). RD's dad would basically be an asshole through and through. In the past him and RD's mom were friends with Fluttershy's parents, all of them making there way into the racing scene. With some unprotected loving, RD's dad loses his dream and the love of his life, stuck with a child he didn't really want. RD's main character point is that she started pushing herself in order to impress her dad, but as she grew older, her motives changed to wanting to get out of her home. This leads her to be rebellious in school.
School life would be as expected; FS would become friends with the more shy people, joining drama club (as a helper), while RD would become popular due to her flying prowess. Gilda would attend the school and RD would get into a rougher crowd. FS and RD would hang out, promising to always be best buds, but would slowly drift apart. At one point RD would miss FS's debut play (after the main actress gets sick, FS would be forced into the spotlight) for some reason (either drugs or hanging out with Gilda). FS would lose her confidence but get through the play. RD would apologize and FS would forgive her, though hold her on thin ice. Towards the Winter break of their final year RD would convince FS to host a party at her house; since her parents are hardly ever there and the house was pretty big and secluded (no pegasi police to bother them), it seemed like the best idea. FS would be reluctant; RD's main selling point was that it would make her popular, but FS only agrees because she knows it would make RD happy. The party goes way out of their control, RD gets high/drunk (though not extremely so). FS gets pressured into sex to 'guarantee her status'. FS slap the guy and run out crying. RD who hears about the commotion a few minutes later would instantly sober up, eventually finding FS out in the woods by her home. They would talk a bit, FS finally tired of RD and their friendship. RD would realize she was being a jerk and set to make things right. When FS refuses to hear it, RD would clear out the party by calling the cops. This would result in her being knocked back a grade and having to attend summer school. RD's 'friends' would get out of punishment by denying involvement, with help of influential parents. FS and RD hardly talk from then on. FS would graduate and go to ponyville to study under the local vet. The epilogue would have RD leaving for another day in summer school before realizing that she needs to start over. She heads for the nearest town, ponyville and finds work part time as weather patrol.
A oneshot sequel was planned to take place after the NMM incident where RD would insist on apologizing. RD holds a lot of guilt towards the past, but secretly hopes that her connection (both being elements) would keep them friends for life.