In one of the issues of the Daken solo series, the title character reads a news article about the new Captain America being outed as Bucky Barnes, the man who killed Daken's mother. He's shown looking at Bucky's picture with an intense stare, and there is a strong implication that Daken is planning on confronting Barnes. The book was cancelled before this fight could occur and Daken never brings it up again in any of his appearances.
The final issue of Dazzler ended with Allison seeking a new status quo, and Beast suggesting that she join X-Factor, the new team he and several of his former X-Men teammates were putting together. Dazzler did not end up appearing in X-Factor, as the plan to have her be the team's fifth member was changed when editorial decided to resurrect Jean Grey and have her be part of the group instead.
Jonathan Hickman's run on New Mutants (2019) ended with Wolfsbane licking Xandra, daughter of Charles Xavier and Lilandra, and giving her a wink. Hickman did not write New Mutants again and eventually prematurely left the X-books entirely, and the scene was never brought up again.
New X-Men: Academy X looked to be building up a Big Bad in mind-rapist Sean Garrison, the Psycho Psychologist father of one of the main characters, Wallflower. However, the original writers on the book were abruptly fired following House of M, and not only was this storyline never mentioned again, but Wallflower was killed in the wave of anti-mutant violence that followed said House of M. The new creative team implied in an interview that Garrison was depowered by the Scarlet Witch's reality warp, but nothing definitive has ever been stated on his fate in canon itself.
During the "Planet X" storyline, The Wasp and Havok had a daughter together named Katie while in the alternate future created by Earth's destruction. Katie was eventually kidnapped by Kang the Conqueror, who used her as leverage to get Havok to play along with his plans. Just prior to AXIS, Immortus showed up and gave the couple hope by telling them they could get Katie back by conceiving a child at the right date and time, which he claimed would allow Katie to be reborn in the prime timeline. Both Wasp and Havok were written out of the series after AXIS, and the subplot was later abandoned entirely once Remender left the book after Secret Wars (2015). The romantic relationship between the two was also ended offscreen by subsequent writers, removing any remaining hope for Katie's rebirth.
Rick Remender's run ended with The Vision learning a horrible secret about Scarlet Witch and refusing to divulge it in order to spare her feelings, and the High Evolutionary claiming that his genocidal actions were meant to safeguard the world from some unspecified oncoming threat. Both plot points were dropped when the book was cancelled and relaunched with a new creative team due to the aforementioned Secret Wars reboot.
Kieron Gillen's Uncanny X-Men (2011) had Mister Sinister as the first villain, and he clearly had more plans in store. In the aftermath of Avengers vs. X-Men, Sinister revealed that he'd been posing as the X-Men's PR expert from even before Gillen's run, and he challenged Scott to stop him once Scott got out of prison — In fact, it's implied stopping Sinister is partly why Scott decided to break out of prison. None of this is followed up on, and the next time Sinister showed up proper, he had a completely new plan involving the terrigen mists.
X-Men has had multiple versions of them: the Baby version of Age of Apocalypse, how Psylocke and Jean Grey switched powers, Psylocke becoming a love rival of Jean's over Cyclopsnote Psylocke and Jean did have a confrontation over it, but it just ended there with no revelation just why Betsy was going after Scott., Carter Ghazikhanian being possessed by Cassandra Nova at the end of Chuck Austen's run, Sebastian Shaw being offered an alliance by a shadowed figure in Joe Kelly's run (identified as the Shadow King by a later sourcebook; Shadow King is the main villain of an arc shortly thereafter, but it's not known what he wanted with Shaw), Magneto press-ganging the Neo to serve him on Genosha (kiboshed by Genosha's destruction the following year), new character Sketch being set up to join the X-Men but then falling off the face of the planet as soon as Chris Claremont left, Kitty Pryde supposedly having some sort of connection to the Neo, the mystery mutant that was present outside the Sentinel base in Uncanny X-Men #57-59, etc. One of the most infamous examples was the "Externals" plotline from Rob Liefeld's X-Force. This secretive bloodline of mutants, all possessing immortality in addition to their mutant power, were built up to be the next big thing, with two former Big Bads revealed to be members of the group, as was a member of the team, whom the others seemed to have various vaguely-defined "plans" for. However, Liefeld left the book before he could tie up all the plot threads, and the next creative team was quick to sweep everything about this story under the rug, with one of the three established characters in the group killing all the new ones and the other two revealed to not actually be Externals anyway. This happened so suddenly that many fans pointed out the fact that the story was essentially Highlander with the Serial Numbers Filed Off and suspected Marvel canned the story to avoid litigation, though Word of God assures us this was not the case. There was also a subplot during Joe Kelly's run that hinted Jean might end up transforming into the Phoenix again. Kelly left the book before this could happen, though Grant Morrison ended up bringing back Jean's Phoenix abilities in their own run. There was also a plotline, dating back to the early nineties, where Bishop referred to Jubilee as "the last X-man", but that plot line has never resurfaced again.
The end of the Jean Grey (2017) series had the younger Jean confronted by her older, modern day self, who said she wanted to talk. This isn't followed up on: young Jean goes back to X-Men: Blue while older Jean goes to X-Men: Red, and the two barely interacted afterwards before the younger Jean was sent back to her own time.
X-Force abandoned several character-centric subplots from John Francis Moore's run as writer when the series was retooled by Warren Ellis. Siryn was possessed by an evil artifact similar to the villain Malice. The team was being stalked by two agents of the Triune Understanding, and Meltdown's father had recently converted to their religion. Sunspot left the team to join the Hellfire Club as the new Black Rook in exchange for his late girlfriend Julia Sandoval being reincarnated in a new body, and it was indicated she was recovering her old memories. There was also foreshadowing that Domino would soon die in a devastating future conflict. None of this was ever properly followed up on by any Marvel series.
In the early 1990s in issues of Uncanny X-Men and Excalibur, there were several hints that Scott and Jean planned to have a child who it was was explicitly presumed would be Rachel, including when Rachel apparently sacrificed herself to save Captain Britain. Ultimately, however, Scott and Jean never actually get around to having kids the normal way (despite having ended up with 4 genetic children in various other ways), and Rachel is brought back through her brother Cable going on a time-travelling mission to find her instead.
X-Men and their spin-off titles have a history of aborted arcs concerning the villainous organization Hellfire Club and their governing Inner Circle.
In 1994, Shinobi Shaw started building a new incarnation of the Inner Circle of the Club. He was assisted by Tessa/Sage, and recruited the new characters Benazir Kaur, Reeva Payge, and Benedict Kine. Kaur and Payge inexplicably disappeared in 1994, Kine disappeared in 1995, and Shinobi himself disappeared in 1997. A storyline hinting towards conflict between this version of the Inner Circle and another one under Sebastian Shaw had no actual resolution.
In 1996, a new incarnation of the Inner Circle was formed through an alliance of the apparently resurrected villains Sebastian Shaw and Selene. They recruited a number of veteran villains, such as Madelyne Pryor, Tessa/Sage, Trevor Fitzroy, and Donald Pierce. This version was the focus of several stories until 1998, when Sebastian Shaw accepted a mysterious proposition by an unseen character and resigned from the Circle to pursue a hidden agenda. The various members of this Inner Circle swiftly drifted away, and various storylines involving their schemes were abruptly dropped.
In 1999, Selene decided to create a more hellish incarnation of the Hellfire Club. She recruited the demon Blackheart, the half-demon Hellstorm, and the corrupted hero Sunspot. Adrienne Frost was also depicted as a prospective member of this incarnation of the Inner Circle. This incarnation lasted until 2000, when it disappeared without a trace. Adrienne died, Blackheart and Hellstorm returned to their solo careers, Sunspot was relegated to behind-the-scenes roles for a few years, and Selene was apparently magically confined to her headquarters until her return in 2005. A storyline concerning this Inner Circle's resurrection of the supporting character Juliana Sandoval, and their plans for her was never resolved.
Chris Claremont's return during "X-Men Reload" assembled a new version of the American Hellfire Club: Shaw as Lord Imperial, Sat-Yr-9 as White Queen, Madripoor regent/international terrorist Viper as "White Warrior Princess", Tessa and Sunspot as Black King. Shaw is deposed, Tessa oversees Sunspot as new Lord Imperial and Viper and Sat-Yr-9 plot something regards Zanzibar and Genosha (as seen in Excalibur #11-13). After House of M, these plots were abandoned and not followed further.
Hellfire Club London was the British counterpart to the American version of the Hellfire Club. It consisted of mostly new characters, along with the veteran villain Margali Szardos. This version was introduced in 1996, and was the focus of a single storyline. They have not been depicted as a team since 1996. Margali was next seen as a captive of the demon Belasco, and most of the other character disappeared.
X-Men: The Last Stand: The Stinger ends with Moira McTaggart discovering that Xavier (who was seemingly de-atomized by Jean earlier in the film) has somehow managed to transfer his mind into her patient, who is otherwise in a comatose state. The film ends with Moira expressing surprise at Xavier's voice speaking to her. Come the next film in the chronological timeline (The Wolverine), Xavier is back in his original body in that film's Stinger, with no explanation given as to how he was able to get his original body back. The whole question is rendered moot by the ending of X-Men: Days of Future Past, which changes the timeline so that Jean never becomes the Phoenix, and is still alive with Scott in the Everybody Lives future.
X-Men Origins: Wolverine ended with the reveal that Deadpool had survived being decapitated, setting the character up for future appearances. The movie's poor reception and mediocre earnings led to the studio completely abandoning any plans for a sequel, and releasing the unrelated The Wolverine and Deadpool instead. The whole thing is later lampshaded in The Stinger of Deadpool 2, where Deadpool time-travels to the events of Origins: Wolverine and shoots Wilson several times in the head before he even has a chance to fight Logan at Three Mile Island.
X-Men: Apocalypse ends with Xavier and Moira beginning a relationship, Psylocke escaping, and the Essex Corporation recovering a sample of Logan's blood from the Alkali Lake facility. While Logan does have a plot thread about X-23, the film takes place 40 years after the events of Apocalypse and no direct connection is made to either the Essex Corporation or Mr. Sinister (the presumed benefactor in charge).
Logan: The Stinger for X-Men: Apocalypse featured the Essex Corporation taking Wolverine's blood samples in a set-up for this film, strongly suggesting that Mister Sinister would be the primary antagonist—or at least the Essex Corporation in his place, who would use Wolverine's blood samples to make Laura. Mister Sinister is nowhere to be found in this movie, however, and the people responsible for making Laura are Transigen instead (presumably through the same methods that the Essex Corporation were employing).note Although nothing rules out that Transigen was not a subsidiary or licensee to the Essex Corporation, as an offhand remark mentions that Transigen is an offshoot of an American corporation. Later statements made by producer Simon Kinberg would reveal that Sinister was intended to appear in a different X-Men movie instead, which would suggest that Essex Corporation is planned for that movie.note The New Mutants, the last X-Men film set in the pre-Disney continuity, confirmed that Transigen was indeed an offshoot of the Essex Corporation, although Sinister doesn't appear as anything except an implied, offscreen Greater-Scope Villain.
Likewise, nothing ever comes of Charles Xavier and Moira MacTaggert reconciling in the same movie. She's not even mentioned.
Western Animation
Wolverine and the X-Men: A significant amount of plot points and storylines have not been resolved due to the show's cancellation.
The Age of Apocalypse storyline, which was going to be the main arc for the scrapped second season.
Professor Xavier is still in a coma.
Colossus never got the chance to rejoin the X-Men.
Angel is currently under Mister Sinister's control.
Master Mold is still out there, trapped in the body of a Sentinel.
X-23 is still in Weapon X's custody.
The MRD continue to pose a threat, even by the series' end.
The X-Men are still rebuilding themselves, even after the X-Mansion incident.
Due to the fact that the series was canceled, Cyclops had never received the opportunity of rising up and redeeming himself and becoming the hero we all know him to be. However, due to that the cliffhanger showed Cyclops would have spent half the season working for the bad guys, it seems highly unlikely that Cyclops would have became the leader again had the series continued.
X-Men: Evolution: Because the fourth season had nine episodes, we never really got to see the conclusion to Legion's (presumably planned) story arc.
There were also a few hints that they would have focused on the Phoenix if the show continued.
Season 3 had a rather heavy Brotherhood presence early on, culminating in Magneto imposing them a new field leader tasked with whipping them into shape and taking out the X-Men... but the "field leader" turned out to be a petty tyrant who wasn't interested in reaching any of his stated goals and the two teams never faced each other again.
"The Unstoppable Juggernaut" ends with Colossus declining an offer to join the team and saying that he intends to travel the country to find Illyana, his missing little sister. The next time Colossus shows up, he's still in New York, and Illyana is safely in Russia with their parents. There's no further mention of her supposed disappearance, and nothing to indicate she's ever even been to America.
In the second episode of the "Beyond Good and Evil" arc, Apocalypse is able to keep Magneto in line by promising to resurrect his dead wife. This is never brought up again, and a later episode of the same storyline instead offers a completely different explanation for why Magneto chose to work for Apocalypse.
The same episode has the Time Traveler Shard say that Archangel is destined to become a member of the X-Men. Despite this, Archangel never actually joins the team in any of the subsequent episodes. This is because "Beyond Good and Evil" was initially going to be the show's Grand Finale, and was planned to end with the team's line-up shifting. When the show was unexpectedly picked up for one more season, the scene showing Archangel and the other new heroes joining the X-Men was scrapped.
"The Fifth Horseman" ends with Apocalypse resurrecting himself by pulling a Grand Theft Me on Cortez, clearly setting him up to serve as an antagonist in the future. And yet, the show never dealt with this before its conclusion.
Likewise, despite "Cold Comfort" having Cyclops and Havok puzzled by each other, including their powers not working, nothing is done with their rivalry or even that they're brothers.
.