Since the strongest message of Fairy Tail is The Power of Friendship you think there would be a strong emphasis on the guild's real strength being working together, but you would be wrong. While the guild does fight together sometimes such as Natsu, Gajeel, and Wendy's fight with the Dorma Anim or the Sirius Team's battle with Hades, there's no emphasis on team work, coordination, or Unison Raid attacks, and it doesn't happen anymore than in, say, One Piece or Bleach. In fights it just means that, just like other shonen manga, that a character will have a flashback, give a speech, or have someone yell encouragment. and suddenly turn the fight around in their favor on their own. The plot generally tends to love giving Natsu one timepower ups to justify him fighting the arcs Big Bad alone or to have him land the final critical blow, in fact, Natsu will often, no matter how high the stakes,actively refuse others help when it comes to fighting.
The Edolas arc. Were you interested to see how the main characters would topple an evil authoritarian government in a parallel world where they're stripped of their powers and have to rely on their alternate universe counterparts and their steampunk technology? Well, too bad! Mashima found it too hard to keep the story going, so he introduced X-Balls to give the main characters their powers back. The off-beat aspects were pushed to the side in favor of becoming what was basically a giant excuse to put Mystoganon a bus. Not to mention, it was the arc that hyped up Lisanna's return only for her to basically remain in the background from then on.
The idea of Lucy alone being able to use her magic gave her and her Celestial Spirits the chance to have A Day in the Limelight, but this idea was quickly dropped and she doesn't really have anything to do the rest of the arc outside of a few fights.
The S-Class Exam trial plot was wasted in more ways than one. Despite the good premise, the execution had problems in places (e.g. Lucy and Cana's fight against Fried and Bickslow ended with their opponents letting them win; Lisanna and Juvia were beaten to a pulp mercilessly by Erza without even giving a good showing, albeit with Juvia being nowhere near her full potential; Loke and Gray's fight against Wendy and Mest was at least pathetic for a partially justified reason...). Another problem was the war with Grimoire Heart interrupting the S Class Exam, when the exam plot could just as easily have been finished first and then moved on to Grimoire Heart happening upon everyone at Tenroujima after the fact, which would have gave more credence to everyone being so exhausted, rather than Erza and Mirajane being exhausted after one fight each that they both completely dominated.
After a 7-year Time Skip, you'd think that the main cast would grow up, looking more mature and badass, and gaining an increase in power. Instead, we got the Fairy Sphere, a defense spell that stops time for everyone on the island by the first Fairy Tail master; meaning everyone looks and acts the same and no visible power-ups. The one minor change was the death of Lucy's father, Jude.
The Revealthat Ultear was responsible for brainwashing Jellal as a kid into his Heel–Face Turn seemed to hint at the possibility of a showdown between the two down the line. However they never cross paths before the seven year timeskip and are shown together as part of Crime Sorcière without any clarification on why Jellal was willing to work with her after what she did to him. One could almost think she never told him about what she did, but than Jellal isn't surprised when Ultear tells rest of the Strongest Team the truth, meaning any reconciliation between the two occurred entirely offscreen during the timeskip. The only thing we get is that Ultear busted him out of prison, but that really doesn't explain anything about how and why he forgave her.
The Raven Tail story-line as a whole. The guild was introduced as far back as the Fighting Festival arc, and was initially presented as a major antagonist being that it was led by Makarov's son, and seemed specifically made to counter Fairy Tail (right down to the name). In the end however, when it does finally get time in the sun, Raven Tail is only one of the participants in the Grand Magic Games where its team spends the whole arc simply bullying Fairy Tail members before at last getting trounced on by Laxus. And after that fallout, it was apparently disbanded.
Jellal joining Fairy Tail's Team B disguised as Mystogan for the Grand Magic Games ultimately ended up as rather pointless since he only gets one fight that he loses and doesn't contribute to the games at all before he gets dropped when the teams are restructured. Him getting a one on one matchup with Kagura would have been a tense and interesting showdown, but they don't meet at all during the games, with Kagura only seeing him from a distance. It feels like Mashima put him in, before realizing his power level would stack the deck in Fairy Tail's favor so he had him beaten early on and sidelined him with his plot relevant events occurring away from the games.
Princess Hisui is revealed to be a Celestial Wizard in the anime exclusive Eclipse Spirits arc, but is never seen using or even owning any Celestial Spirit Gate Keys.
During the Sun Village arc, Minerva mentally claims to have a counter to Erza's Nakagami Armor. What could possibly help her against such a powerful armor? Never mind, Minerva's good now. Speaking of Minerva, she and her father both undergo demonization. Many were expecting new powers, or even an Etherious Form. Both are defeated in underwhelming battles without showing anything new.
While Silver Fullbuster is beloved by the fandom, many wish that Silver was actually Deliora in Silver's body like he initially lied about. Not only would that allow Gray to confront the monster that ruined his life, but it would let him get a chance at developing and provide a good emotional moment for Gray to avenge his mentor and family after generally being Out of Focus since the start of the series. What the audience gets instead is considered good for the most part, but many feel it lacks the same emotional weight as him being Deliora, especially since Deliora being able to come back and get revenge would have fit nicely into the arc since he his death occurred in a way that could easily justify him coming back. Plus Silver could still have gotten a chance to say goodbye before dying if they wanted to by having him momentarily regain his body to say goodbye to Gray, and still pass his powers on.
Chapter 363 implied that other guilds would be coming to help Fairy Tail against Tartarus, potentially leading to an all-out war similar to the Dragon King Festival, except that this time, more than seven people would be able to do some damage. The only guild that ends up coming for assistance is Sabertooth (and even then, only the Twin Dragons). The arc ends up with only Fairy Tail fighting, and even then, only the Tenrou Group gets in on the action. The anime, at least, shows all the other guilds dealing with FACE in their own towns.
This is especially bad with Crime Sorciere. They have an interesting plotline set up at the start of the arc with Jellal recruiting the freed members of the Oracion Seis to combat Zeref. It look like they were headed to aid Fairy Tail in the fight against Tartaros, teaming up with their old enemies against the Dark Guild. Than.. they do nothing relevant for the rest of the arc, only showing up a week late in the epilogue so Jellal can exchange a few words with Erza. At least the other guilds tried to stop the Faces, while Crime Sorciere acomplish nothing useful.
Ikusatsunagi in Chapter 433 & 434 would have been a great chance to make the God Slayers actually relevant as a setting element, especially Chelia/Sherria, who might actually have a reason to get involved and to have followed the group. Instead it ends up being a one-hit kill on Natsu's part. Then Chapter 476 released and something happened that either made them relevant or made them more insignificant.
While we're on the topic of the Avatar Arc, the revelation from Future Rogue that the one who killed Frosch in his timeline was none other than Gray. Indeed, Gray seemed to have had a Face–Heel Turn(even if he was actually The Mole for Erza), but at the end of the arc, when the two of them were face to face, Gray just spazzes out and hugs Frosch for being so cute. There is absolutely no explanation as to why the Bad Future was averted, or which event Set Right What Once Went Wrong, leaving fans wondering if Natsu showing up was all it took to avert the Bad Future, or if it was Gray needing to save Lucy's life, thus blowing his cover and the need to keep up appearances, with no real answers to satisfy how and why Frosch was saved... or if it merely delayed the inevitable. When asked about this plot point in the Fourth-Wall Mail Slot, Hiro more or less admits that he didn't think through how he was going to implement it and consequently dropped it.
Erza becoming the Seventh Master. She's one of the most powerful members of the guild this side of Gildarts, has obvious leadership skills, and commands the respect of the entire guild. She was more than qualified for the position, and pretty much the entire fandom was eager to see in which direction she would take the guild. She only oversees one mission, which, while successful, resulted in a Tactical Withdrawal. So what happens when Makarov comes back? Makarov becomes guild master again. FOR THE THIRD TIME. Status Quo Is God indeed.
Natsu and Gray's secret weapons during the Alvarez Arc. Natsu's was Igneel's magic power, which doesn't really amount to much more power than Natsu had already displayed in the first few chapters following the second Time Skip. Gray's was Iced Shell again, simply with the added effect of making him Ret-Gone so nobody would remember his sacrifice. Not only was this a disappointment for those who expected something bigger, but it also displayed a huge case of Aesop Amnesia on Gray's part that Natsu himself brings up from Galuna Island.
The revelation that DiMaria is a Racial Remnant of the people of Mildian opens up a multitude of possibilities, especially considering the city is stated to have later worshiped Chronos, the God of Time, of whom DiMariais basically a living vessel with her Take Over ability. Perceptive fans have noted that this is also the same city where Zeref attended school up until receiving his Curse. When did Mildian become the home of Chronos, after its populace used to worship Ankhseram? Was Mildian actually located within what is now the Albareth Empire? And if so, does Zeref have something to do with the conversion, and is it really just a coincidence that a descendant of Mildian now serves him? Does DiMaria know that she's now serving the same person who started Mildian down the path of destruction, or does she even care? All of these unanswered questions make it seem as if the Racial Remnant revelation was added on to DiMaria's backstory as an afterthought, which is a real shame, because not only could it tie into the backstory of the Albareth Empire as a whole, but also potentially Zeref's.
The Reveal that two of Irene Belserion's henchmen, Juliet Sun & Heine Lunasea, are fake personas that Irene brought to life as Living Weapons really brought to question if Erza was perhaps one as well given that there was an obvious connection being build up between Erza and Irene. Instead, Erza turns out to be her actual daughter, and by extension is the daughter of the former Dragon Queen, which for some is still a plot worth pursuing, but to others looks like it came (though more for the second point than the first, which would be a Captain Obvious Reveal).
Irene hijacking Wendy's body. While nobody actually expected it to stick, it presented the possibility of a real plot conflict; can Fairy Tail really bring themselves to fight one of their own, even if she's not herself? Could Irene have used Wendy's body to find a clue to reversing dragonification? Would Zeref have been able to use Wendy's Milky Way magic to speak with Igneel, or even Belserion to find an edge against Acnologia? We'll never know, because it was reversed one chapter later.
Natsu being an Etherious, more specifically Zeref's most powerful creation E.N.D., laid the foundation for several promising plotlines that ended anticlimactically. Gray's personal grudge against E.N.D. led to a fight with Natsu, but Erza's intervention prevented that from being resolved one way or the other. Natsu dying from the Demon Seed and Dragon Seed inside his body forces him to decide which he wants to be, but Natsu just deciding to be "human" destroys both seeds and wastes all the drama the plotline gave it.
Jellal never getting a chance to face off against Zeref is a major one, considering how Zeref's would-be followers massively screwed up his life by enslaving him as a child in the Tower of Heaven and brainwashing him into a deluded cultist who tried to sacrifice Erza. It's even lampshaded in story, with Zeref noting he expected Jellal to get there first and is somewhat disappointed.
The Reveal in Chapter 526 that August was actually the true child of Mavis and Zeref, and not Larcade, caught many people off-guard, and had the fanbase invested in the story wondering where this plot-line was headed. One chapter later, August decides to kill off Fairy Tail along with himself, but stops when he sees Mavis dying from the spell and instead sacrifices himself without killing anyone else to spare her. While providing an extremelyemotional scene, many in the fanbase wish that this revelation could have provided more before that point.
The drama of Natsu dying if Zeref dies has an unsatisfying resolution. After Zeref stabs Natsu, Lucy repairs the hole in his chest by rewriting his book, and begins to suffer a corruption from tampering with it. This could have led to Natsu's life force being tied to Lucy's instead of Zeref's, but the corruption is dealt with by Gray's Ice Devil Slayer magic so easily that it might as well never have happened. Ultimately, Lucy writes some vague additions to Natsu's book, and the consequence of Natsu dying with Zeref is unceremoniously averted.
The brief subplot involving all the girls of Team Natsu (as well as Happy) being turned into yokai was resolved quickly, in just a couple chapters (Erza was reverted to normal in the same chapter her yokai-form was introduced), and without much drama or trouble. To some, this was a major missed opportunity, particularly for development between Lucy and Natsu, whose relationship has remained otherwise underdeveloped compared to the other characters, while the conflict of Natsu and Gray being forced to technically Staking the Loved One would raise the stakes and make the subplot more engaging. Amusingly, In-UniverseSelene herself seems to agree given how quickly her mood sours at the sight of everything wrapping up so quickly and neatly.
