Acceptable Religious Targets: The Fellowship of the Sun is full of vampire-hating people who feel it's their right to tell people how to live their lives. They also preach vampires and other supernaturals are an abomination in God's sight. They're not above blowing things up or killing people to make this point.
Alternative Character Interpretation: Sookie - An unfortunate woman who's been "Crazy ol' Sookie" for so long she doesn't know how to be anything else or a professional victim who doesn't want to be anything else? Is Sookie a hard-working, innocent woman, brought into a world she doesn't belong in and ends up having her heart broken by many men? Or is she just a nosy shrew who keeps putting herself in these situations, and cruelly toys with her men and breaks it off with them whenever she gets pissed?
Anti-Climax Boss: Sookie accidentally sets up Claude's downfall by mentioning he's gay. This leads to his minions, Johan Glassport and Steve Newlin to turn on him, allowing Sookie to escape. A nameless minor character shoots Claude about two pages later.
Anvilicious: We get it, Charlaine Harris, it's a metaphor for gay people and how they are treated. The books may also be poking fun at using mystical creatures as metaphors (elves, zombies etc.). Hell, Eric even calls Sookie out on using a bad metaphor (comparing vampires to lions) in the fourth book.
Base-Breaking Character: Sookie's become this in later books. This is in large part due to shipping as her relationships move increasingly away from Eric (and to a lesser extent Bill) but also due to her perceived lack of character growth. Many fans criticized Sookie for feeling like she largely ended up in the same place she was at the start of the series and because of her increasingly judgemental internal narrations, making her unlikable to many.
Broken Aesop: Vampires are treated as a metaphor for LGBT+ people and their struggles. However, as many fans point out, vampires are dangerous, including the nicer ones. This feels further broken as Sookie herself grows disillusioned with vampires and vampire politics.
Sookie ending up with her boss, Sam in the last book. While some fans were unhappy with the ship itself, even shippers found the lack of build up dissappointing, particularly they only hook up in the last book. Not helping is the fact that Sookie and Eric, a Fan-Preferred Couple for much of the series, break up in the same book, leaving little time to give closure to that and establish Sookie and Sam.
The conclusion of arranged marriage contract plot with the Queen of Oklahoma. One of the big sources of conflict in the last books is whether Erik and Sookie can break the contract his maker made for him. Though Sookie and Erik agree to fight against it and the queen is introduced as a possible antagonist, Erik ultimately goes with her. On one side you have shippers upset at the Ship Sinking and that the characters didn't even part on affectionate terms. On the other you have fans horrified that not only is Erik being controlled by his abusive mentor beyond the grave but also that he's stuck bound to another vampire for 200 years.
The emphasis on character and romantic drama rather than mysteries towards the end of the series. Though these elements were a constant part of the series, it was balanced with mystery and plots involving the supernatural community. Towards the end of the series, much of the action is instead handled quickly or off-screen and the mysteries lackluster.
Creator Backlash: Charlaine Harris wanted to end the series with Dead and Gone but was effectively forced by her publishers to continue the series due to the ongoing popularity of True Blood. This, combined with the fact many fans confused the series with her books, resulted in her getting increasingly fed up with it. Some people believe this is why the final books were so harsh and against the characters.
Bill is one of the more polarizing suitors. He's seen as a controlling, emotionally abusive stalker who will never live down the fact he started a relationship with Sookie under false pretenses and raped her while he wasn't in the right mind.
With the end of the series, Sam is hit by this hard, given the fact he ends up with Sookie.
Ending Fatigue: The tail end of the series is less about the mysteries and more about giving closure to characters and storylines. Due to having so many characters and having to shoot down Sookie's chances with love interests, this takes several lengthy books.
Ensemble Darkhorse: Pam and Bubba. Hunter's also become one, having been the focus of speculation and fanfics.
Amelia. Many people are miffed at the thought that she might not be adapted into the TV series.
Ho Yay: Jason and Hoyt, Jason and Mel. Deliberately on Mel's side, because he's gay.
And, In Dead In The Family, Claude and Dermot, two of Sookie's fairy relatives. Claude's actually gay and Dermot is...questionable. They sleep in the same bed at the end of Dead In The Family, albeit with Sookie. The book ends on this mildly incestuous OT3 image.
Not forgetting Mustapha and Warren. At the end of Deadlocked, Sookie is literally left "confused" by their open display of affection.
Nightmare Fuel: There are several instances of torture and/or particularly gruesome deaths.
Strawman Has a Point: The anti-vampire cult that wants to destroy vampires because they are inevitably evil predators guilty of at least one casual murder, initially presented as the equivalent of various real-world anti-gay movements... is entirely correct in their assessment and makes a good argument in favor of their course of action. This is lampshaded occasionally by Sookie, who recognizes that her motives in keeping the truth from the normals are selfish and probably amount to abetting murder herself, and becomes a plot point when one particularly ancient vampire initially agrees with their plan to the point that he's willing to help them out even though it means dying himself.
Tear Jerker: Adele's funeral. It shows how beloved she was in Bon Temps.
Nothing much ever comes of Sookie's occasional ability to read vampire minds when it could have been an interesting source of conflict, particularly as Sookie is aware of the fact that, if vampires knew, it'd be dangerous for her.