These are what we call the 'YMMV items.' Things that some people find in this work. We call them 'your mileage might vary' because not everyone sees these things in the same way. This starts discussions in the trope lists, a thing we don't want. Please use the discussion page if you'd like to discuss any of these items.
Crosses the Line Twice: While writing Part One, the author picked up the line and played jump rope with it. While writing Part Two, he drove past in a car with a rocket-powered engine, obliterated the line, and never looked back.
Family-Unfriendly Aesop: It is your responsibility to make your friends atone when they've wronged someone else. So how should you go about doing that? Why, Mind Rape them into thinking they're babies again, of course!
Here's another, this time directed at Dash: Trust no one. They're all out to get you.
And yet another, for Fluttershy: Want a baby to raise, play with, and sing to, but you're too lazy to go through the red tape of adoption or child birth. That's alright, just Mind Rape your best friend!
There was also a Pinkie Pie baby doll that was released some time before the Rainbow Dash one.
Idiot Plot: At one point in Part 1, a still unregressed Dash is let completely alone and unsupervised by Fluttershy. Yet she didn't take the opportunity to either escape or set a trap to give Fluttershy her own Tap on the Head.
Inferred Holocaust: Let's just say that if Discord ever goes against his word and becomes evil again, it's gonna be a cakewalk for him to ruin Equestria, what with Fluttershy being the only Element of Harmony left still in control of her faculties.
Internet Backdraft: Bring this fic up and just about everyone will be united against it even more than they were about Cupcakes.
Moral Event Horizon: Well, once you've committed Mind Rape and then done everything in your power to keep your victim as permanently damaged as you can, there's really no backtracking. Fluttershy just plunges forward becoming more ruthless, going from slipping mickeys to [bashing victims in the head with a pot; from general baby treatment to making ponies run a gauntlet of death traps; from fixes of foalmula intended for temporary effects to doses inducing everlasting ones.
Nausea Fuel: There are a few needlessly graphic descriptions of adult diapers being filled and changed. Bleh.
Squick: Big Mac and the Mayor are even into Fluttershy's fetish. Big Mac. And. The Mayor.
Also, there are several fairly detailed descriptions of diapers being filled. Bleh.
The Woobie: You really can't help but feel horrible for Rainbow Dash and Scootaloo throughout the whole story, moreso after they are exposed to the Foalmula, rendering Rainbow, if not both of them, infantile forever.