Badass Decay: Leonard's fans thought so, after Lori and her coven used "plan BC" on him. After which, he all but became their slave, since Lori made him their thrall. The following arc, he seemed to return to form, when he briefly helped the PMS during the prom and, later, helped rescue the cheerleaders from Cressida Harrow - only to revert to merely being an everydude.
Broken Base: The merger of the two strips split the fanbase into two factions, along the exact lines you'd expect (mostly covered in the Rooting for the Empire entry).
The "Vampire Cheerleaders Must Die!" arc upset fans of the cheerleaders, since the PMS were cast as the heroes and were ultimately the victors. Which caused many of them to drop the comic (see the trivia page), while fans of the PMS crew felt the comics should've remained separate, since they didn't care for the cheerleaders.
The fans took a shine to Leonard and the Bakertown B squad, mostly because they have more likable traits in comparison to the Vampire Cheerleaders.
Suki was chosen to represent the cheerleaders' side for the comic's final volume, because she was the one the fans liked most - between her ditzy personality and because she was the nicest toward Leonard.
Heather did a swan dive over the MEH in the very first chapter, after readily accepting her change into a vampire. The first thing she did with her newfound power was turn on her own parents and reduced them to being her mindless slaves. Up to and including forcing themto make her a baby sister. Earlier on, she even asked when they were going to kill people.
Bianca Harrow raped and tortured Lori for days, while Lori was powerless to defend herself after being paralyzed by Bianca's stare. And when her sister, Cressida, found out Lori had killed her, she flew to Miami, where she tortured and killed Bianca's servant in the cruelest way possible.
Rescued from the Scrappy Heap: Vol.4 paints Suki, Zoe, and Lesley in a much better light; showing them to be fairly decent individuals. Including treating Leonard much better than in previous parts of the comic.
The contempt for Heather's character is near universal among the readers; including fans of the vampires. But you know it's bad when Shelfer (the artist for series since vol.3) admitted even he didn't like her and didn't even like drawing her (noted on the Trivia page).
Many didn't like Lori even before the merge with Paranormal Mystery Squad, due to turning Leonard into a thrall, and being an Alpha Bitch in general. But when she all but single-handedly curbstomped the PMS crew and near fatally bit Char, the fans lit upthe forums.
Strawman Has a Point: Many readers sympathize with Marcy's point of capturing and treat cryptids in a more humanitarian way, especially in light of the summary execution Steph delivers early on, even though she doesn't seem to care for the victims of the cryptids, considers any instance were a cryptid was killed as unnecessary, not caring for the circumstances, and just tries to impose her ways over everyone else.
They Wasted a Perfectly Good Plot: There was a lot of potential for a story involving Leonard trying to expose the cheerleaders as vampires, and Heather being torn between her loyalties to her fellow vampires and that of her friend. Instead, Leonard gets turned into a thrall, character development is safely avoided, and the PMS has to come in and solve everything.