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.
Hype Backlash: Was somewhat inevitable given the fic's popularity. Take a good look at the like/dislike ratio of the sequel and compare it to the first one.
Squick: Though it is all handled very tastefully, the relationship between Peter and Twilight has taken a decidedly physical turn of late, and even if the whole Interspecies Romance thing doesn't bother you, Twilight Sparkle's such an adorkable, innocent character (in this story as well as canon), that seeing this side of her can be a... unique experience to say the least.