Badass Decay: In his first appearance Bismarck was able to hold his own against Suzaku, Schneizel and Cornelia all at the same time. Come the Grand Magic Games, he gets his ass soundly handed to him by Asura, Shimon, and Erza.
Kagura and Jellal as a pairing has left fans divided. Some believe it's much better and well-developed than the canonicaly implied Erza/Jellal, while some believe it's ever worse.
While Mordred as a character is a class example, a decision regarding the character split the fanbase and even gave the author pause. As it later turns out, Mordred is the name of the demon within Future Lelouch and nudged him into doing reprehensible things, thereby lessening the impact of seeing Lelouch at his darkest. The author even acknowledges this drawback, defending that he feels the pros simply outweigh the cons, even finding that he made Lelouch too evil. Of course, his fanbase is split on this.
Same goes for Mordred, but the author knew better than to change horses mid-stream. Even if the reveal fell flat, it doesn't change everything else about the character.
Complete Monster: Dark Lord Sabine aka Margaret Fernandes. She raped a man, which got her pregnant, sold said child Jellal into slavery at the Tower of Heaven cares about nothing except becoming queen, which she believes to be her birthright and has been called a sexual predator by at least one reviewer. As if to hammer the point home, Zancrow, considers being adopted by her to be an honor.
As of chapter 100 it's then revealed that she considers what she did to Jellal trivial, which only further cements this trope.
And then in chapter 101 we get insight to her backstory, completely defying any chance Margaret had at having a Freudian Excuse, thus making her this trope to pretty much almost everyone.
Ensemble Dark Horse: Sindel and Airy are well-received by the fan base at large, even voting them into the Fairy Tail Team B for the Grand Magic Games more often than some of the canon cast members.
Emma Jaeger is also a very popular villain and some fans can't wait to see her come back. In fact her entire involvement in the Envoy of the Future arc is described by Draconic Hero as Fanservice since he had no intention of originally putting her in the arc until fans asked for her.
Foe Yay: Rakshata and Lloyd are still trying to one up each other. Laxus and Gajeel even comment to the effect that they should do the sideways polka.
If the writer is to be believed, he had the scenes with Juvia and Gray in Gildarts' summer home planned out far in advance, making the scenes in the Avatar arc an example of this trope.
Storm Dragon Slaying now that it's been revealed that God Serena can use it as an element in canon.
Ho Yay: The author wasn't even trying to be subtle with the scenes between Orochi and Hibiki at one point describing Hibiki stripping in front of Orochi as an uke giving into their demanding seme.
Female example: Kallen and Sachi certainly had their moments. Nonette and Cornelia get this a lot and even Milly and Shirley have a touch of this. Right now Nina seems to be one-sided regarding Euphemia.
This is taken to its logical conclusion Up to Eleven in Mermaid Heel.
On the subject of Mermaid Heel, fans have started to cry for Tamara from that guild with Legretta from Phoenix Grave as a potential pairing.
Moral Event Horizon: Many reviews for chapter 193 followed a pattern of "any sympathy I had for Mordred went out the window for attacking Nunnally" doubly so given that Mordred is Lelouch from the future.
The Scrappy: Suzaku's Lawful Stupid nature in chapter 74 has made him this to a lot of readers. Some Suzaku haters have even said that they hate this verison more.
What an Idiot: Sometimes the more...innocent characters of the series can drive you to facepalm
Euphie, sweetie, being in a relationship with someone isn’t going to stop the Male Gaze
NINA! YOU FUCKING IDIOT! Euphie had the situation with Kallen under control!
Estellise has so many that we’d be here all day listing them.
The Woobie: Outside of Knightmare Frame you have Undine Celeste, the guild master of Mermaid Heel who was taken in by Erubay, the water dragon. Erubay, an otherwise humanhating dragon, took her in and raised her, but when Undine ran off after discovering another human, eventually being asked for her hand in marriage, Erubay killed her fiance and Undine became so enraged that she wound up killing her own mother. If that wasn't bad enough, since she doesn't have the dragon anti-bodies that were given to the other dragon slayers in canon, she is slowly turning into a dragon and her arms are the first victim on her body. She has also regretted that day of her life for the last 23 years and counting. At least one reviewer of the story has admitted to wanting to give Undine a hug.