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.
Archive Panic: This webcomic started in January 2000. According to the archive, it's been updated almost every day... for 14 years. At about 350 (or so) comics a year. Not as bad as some of the other examples on the Archive Panic page, but getting there.
The Patriarchy plot, not necessarily because it's a hard plot to swallow in itself, but because of how suddenly and powerfully it appeared, and also when compared to the strip before. The main issue now seems to be members of the Sisterhood saying blatantly offensive things, like advocating unprovoked violence against men, when compared to their previous characterization of being a small Jerk Sue organization. Because of this, along with the outright demonization of men that would make a Lifetime Movie of the Week writer shake their heads (such as having Xanthe get bombarded with garbage by a small army of background strawmen and then claiming in an attempted Tear Jerker that "male allies don't exist"), male readers who would otherwise be supportive of the storyline feel the strip is actively pushing them away. The strip has even been likened to some of the more clueless social justice blogs from Tumblr in comic strip form.
Many fans are also turned off by the fact that the writer tends to handle any and all criticism of the Sisterhood by apparently assuming they're just misogynist jerks, dismissing their (often reasonable) complaints and labeling them as "dudebros" who are really just whining because Monique doesn't shake her ass anymore. We know this because dozens of strips are dedicated specifically to the purpose of taking common complaints about the direction the strip has gone in and having the designated strawmen Slick or Squig say it, probably while crying and probably after having twisted it into something blatantly misogynist. Another form this takes is in having Monique put on magical "patriarchy blocker" glasses that "translate" common criticisms into something easier to dismiss.
The original concept to begin with, as used to imply that Christianity rang more true than the other religions (even as characters like the Buddha and the Dragon walked around).
Base Breaker: Xanthe, and the whole Sisterhood plot in general for stealing the spotlight from most of the cast in general. To some it has been labeled as when the comic Jumped the Shark. Her degree of polarizing effect is so bad that she can accurately be compared to Sasuke (stateside only) and Miko in terms of how divisive she is.
Bile Fascination: What keeps many people reading the strip following the introduction of The Sisterhood. You'll find a heaping pile of it on display if you visit the TV Tropes Forum page about the comic.
Black Hole Sue: Xanthe, again; her actions and their results have been taking the spotlight for what some see as a disproportionate amount of time. Not to mention that practically every other character has undergone a major change or all but vanished since she was introduced, and most of the changes have been caused by the Sisterhood or can be linked to it (like the Devil changing in order to become the one behind the Patriarchy).
Broken Base: The fandom got along relatively peacefully, but that changed starting around 10/2011. Nowadays it's gone into fandom civil war-grade fracturing.
Canon Sue: The Sisterhood, especially Xanthe: always right, always victorious, always morally superior, with the story now revolving around their mission. They're also the Devil's current Arch-Enemy (because he apparently doesn't have any other projects than encouraging patriarchy), with Buddha, Jesus and the angels gone, and God (while mostly absent too) being a chauvinist who needs correction too.
Xanthe and her cohorts, to those who don't like her. See Base Breaker above. She and the Sisterhood story arc shows up in 1 out of every 5 strips. note 1-of-5 is as a whole. In practice, the storyline will have a huge percentage of strips focusing on it in a fairly short time period. For instance, since about May, the Sisterhood plotline has more or less made another attempt at taking over the strip, as about half of the strips since then have focused on it.
Ho Yay: A few strips on bromance get pretty close to this, but the most obvious is Lil'Evil and his feelings for Satan... until we learn that Lil'E is actually the devil's son.
His crush on the Devil is rather transparent.
Goes beyond transparent to explicit in this strip. He likes the idea of spending eternity "locked in homo erotic embrace with the devil."
May actually be a case of If It's You, It's Okay or even Single-Target Sexuality, seeing as he doesn't really act that way over anyone else, male or female, and often talks down to the oversexed or hormonally frustrated main characters.
Irony: Xanthe described gender roles as source of discontent and alienation, however it was exactly "enlightening" 'Nique that led to discontent and alienation of 'Nique, who actually stopped feeling comfortable in her life, descended into paranoia and was condemned by her fans as a result of a change in her views. Despite author's mockery, the same could be said about Slick who now, due to the change in 'Nique's ideals, lost an important friend.
The Devil and Lil' E now that we get to see some of their backstory.
Jerk Sue: Xanthe. She never gets called out or suffers bad karma for her behaviour.
One could argue that Xanthe doesn't really do anything particularly jerky. She tries to enforce her Ideals in a similar-ish fashion to Seymour, but is much more passive about it when compared to him really. She spends more time encouraging females than she does attacking males, which is the kind of behaviour that would really push her to Jerk Sue levels. It should however be duly noted that the 7/5 strip shows in a darkly ironic way that she's every bit as sexist against men as the Patriarchy is towards women. Namely due to, as many Peanuts fans point out, the behaviour of Sally towards Linus is far worse than Chuck's is. This point does point her more towards being a Jerk Sue.
What hurts her case even more is that the author is clearly more sympathetic to her views than that of Seymour. It may not truly be to the point of using her as a mouthpiece and hell, a lot of her points really make sense, the massive amount of exposure she and her cause have gotten in the past year, plus the fact that the vast majority of it is portrayed mostly positively indicates that she's supposed to be at least "right" in a lot of her points.
In a way, the recently enhanced extremism of the Sisterhood may be an attempt to avert this, by giving them some actual negative qualities that are meant to be disagreed with, like advocating violence against men. The problem with this is that they were portrayed as nigh-flawless and always morally superior to everybody else (even to God), and a pretty blatant mouthpiece. So to suddenly change their characterization to be more flawed and realistic simply makes it look like the mouthpiece is now advocating morally reprehensible things.
Jumping the Shark: A common complaint, leveled at most things involving the Sisterhood.
Mary Sue: The primary complaint about the Sisterhood, especially Xanthe. They get progressively more blatent with further strips.
The Devil himself, who'd had Jesus as his Butt Monkey several times, is unable to beat the Sisterhood even once, and, worse, he can't find a way to benefit from their movement (other than letting others assault them), leading to the conclusion that it's some kind of epitome of moral perfection.
Moe: Criminy, Fuchsia, Pooch, Percy, Squig, Buddha, Angie/Tange, Absinthe, and the enlightened Illuminati Drones are all kinds of cute.
The new drones after the Devil rebuilds his factory. Everything funny and cute that took down the drones before, like Cupid's arrows? No longer work. The new drones even look creepier and more insectoid.
And on that note, with Seymour becoming a whole lot nicer recently (he even brings snacks to Lil' E and Pebbles) he's been rescued from the heap as well.
Romantic Plot Tumor: Arguably the Fuchsia/Criminy romance, although a quick look at the Characters page, the Awesome page, the Heartwarming page, and even the main page will tell you that it seems to be the most referenced, popular story arc in the comic.
Rooting for the Empire: The Patriarchy arc seems to have provoked this reaction due to just how polarizing the Sisterhood (Xanthe in particular) is.
Stop Helping Me!: Fyoosha has tried on-and-off to get Blue to reform as well. The first attempts were shot to hell, and Baby has lost all patience with the concept of redemption. Fuchsia won't take the hint.
Unwittingly or not, Slick does point out one of many complaints people have about the Sisterhood in this strip; namely, that Monique's characterization has drastically changed since their introduction.
In "Victim Blaming" Slick (clumsily) points out that if you say things to rile people up, they're going to get riled up. If he'd just suggested making the same points but in a more nuanced fashion, rather than an Anvilicious one, it might have gotten through.
This strip which has Slick singing cheerfully about the joys of misogyny overreacts at a protest sign carried by a Trike Girl and calls her a hater. The problem being that the same Trike Girl was recently in a comic cheering out for the death of all men, making Slick Accidentally Accurate in his overreaction.
Tastes Like Diabetes: The longer this strip runs, the more horrifingly adorable it gets. And then we have...
They Changed It, Now It Sucks: Part of the problem with the Sisterhood plot is the strip shifting from skewering all examples of extremism to ignoring its own message when it comes to feminism. Before the Sisterhood plot began, fundamentalist religious beliefs, consumerism, and other extremes of belief and behavior were heavily parodied in a manner promoting a moderate perspective. However, the feminist extremists of the Sisterhood are always right and there's no longer a middle ground.
To some, it's an even simpler explanation: The Sisterhood is such a Plot Tumor that it's damn near omnipresent in the strip now. Overall, something like 20% of the strips since its introduction have focused on it, and it's even more counting how many strips have involved it by extension or focused on the results of its actions, which would be something more like half of the strips. It isn't whether the Sisterhood is right or wrong, it's just that most of the other storylines have been so pushed aside in its favor and even then will usually involve it when they're brought up.
Many fans also hate just the massive changes that the Sisterhood has brought on, leading to accusations that Xanthe is a Black Hole Sue. Slick changed from a mildly misogynist, but well-meaning idiot who had a thing for a specific girl into a fully misogynist Jerk Ass, whose sympathetic qualities seem very unintentional. Monique went from a reasonably ordinary woman who was trying to overcome her Attention Whore traits to a borderline paranoid wreck who now mostly just wanders around the setting mumbling about the Patriarchy (this one is particularly damning because it was caused directly by the Sisterhood, as opposed to the others who were changed by "coincidence"). Squig went from a harmless hedonist who was also a bit of a perv to a strawman for the anti-pornography Sisterhood to use as a punching bag.
The Sisterhood has also pretty much erased the relationship between Slick and Monique. While they were once attempting to get together, this has seemingly been forgotten in favor of Monique being paranoid and Slick being the Butt Monkey to the Sisterhood. This is especially damning because some considered this to be the central plotline of the entire strip, which has not only been pretty much set back to square one, but is now barely mentioned, and all of that Character Development they earned over the course of roughly eleven years has all but vanished. The strip also attempted to portray Slick unsympathetically for wondering why his former love interest was acting so strangely and no longer seemed to want anything to do with him.
Ugly Cute: The zombie and his attachment to Fuchsia.
Uncanny Valley: Characters that walk into the Reality Zone can come off as this at times.
Increasingly, the people targeted by the sisterhood who actually make good points; see Strawman Has a Point, above.
Unintentionally Unsympathetic: The sentient Fembot. The viewers are to sympathize with it because its aware that it only use as a sex object. All good. Except that most of it's screen time is it being very violent against people, borderline Killer Robot, which has caused it to get the nick name of "Maverick".
Just look at how she (and the "adorably" innocent Pebbles) reacts towards a man with the audacity to wish the "ladies" a good day — which is sexist now, apparently: Behold and Enjoy/Rage.