Gilda is either a terrible friend to Rainbow, or a good friend to Rainbow who nevertheless gets annoyed with her (and prioritizes her relationship with Billy).
Billy (and by extension, the other bullies as well) is undeniably a Jerkass who's just dicking with Rainbow For the Evulz, and has received no comeuppance besides a threat or two. The broken base is about whether this is old and annoying and people want him dealt with already, or if he's interesting and has a shot at redemption (and then there's the smaller broken base about whether or not he should be redeemed).
Fluttershy, up until she got together with Brolly and promptly went Out of Focus, was either The Woobie or served no purpose except to be cute and draw sympathy. Nowadays people are either glad or upset that focus has shifted to Rainbow.
Broken Base: The heavy foreshadowing regarding Derpy's apparent pregnancy with Dinky. It's granted a lot of sympathy for her from some readers, but others have started to get sick of it and feel that it's started going overboard.
Whether or not the comic should become its own thing as an "alternate universe" type deal* to allow for the current relationships, romantic or not, to remain as they are or eventually weld itself with the show's canon * which would break up Rainbow/Firefly and Fluttershy/Brolly, and since Rainbow dropped out or was kicked out of flight school in the show's canon, presumably lead to a Downer Ending. Supporters of the former don't want to see all these characters torn apart from each other for various reasons, supporters of the latter want to see how the author would lead things from their current state to the one the show provides.
The numerous ongoing plot threads either make all the going-ons of the comic too complex and annoying to follow, or make it intriguing and gripping. Of course, even people who believe the latter take some issue with it due to how long each comic takes to come out, requiring a fair bit of catching-up to remind oneself exactly what was going on last time when a new page is released.
Darkness-Induced Audience Apathy: More sad-related darkness than most examples, but with all the drama going on - Derpy's pregnancy, Rainbow and Gilda's failing friendship, Billy and his friends being the usual bullies, Rainbow and Firefly keeping their relationship secret (and implications that, after school, they'll have to split up), Gilda's relationship with Billy seeming to be an unhealthy one, the JV Team trying to work through it all - many readers have reached the point of just getting irritated when something else bad happens, rather than shocked, and just want to see the bad guys get their karma and the good guys finally get to relax.
"Funny Aneurysm" Moment: At the very end of Chapter 4 there's a brief scene of Pokey hitting on Derpy as an amusing little Fandom Nod to Dinky often being portrayed as Derpy's daughter. Come Chapter 5 and it's hinted that he apparently had a one night stand with her, leaving her pregnant with Dinky. Chapter 6 pretty much confirms it, and he got her, an underage student, drunk first to boot.
Derpy and the Pineapple. Oh Derpy, you needed better sex-ed than that.
Rooting for the Empire: For a while, people were on Billy's side, since Rainbow was being a Jerkass herself. Subverted after a while, since even though people still like him, good luck finding anyone who actually wants him to come out on top against Rainbow.
Rescued from the Scrappy Heap: Dash's behavior in the second half of chapter 5 was enough to make up for it for most of the fans after her prior outburst.
The Woobie: Fluttershy, unsurprisingly, and Derpy. Especially after the fifth chapter.