DS and Mezzo's 20th and 16th birthdays respectively occur during the time they're stuck in the mindscapes.
PEFeDOS during the PMD-R arc is awakened and begins her sadistic testing once again on Tagg's 21st birthday.
It repeats with Tagg ending up in Ransei 600 years in the past due to concentrated April Fools shenanigans on his 22nd birthday. Herbert, also in the same situation, has his 16th birthday the next day.
Straw gets attacked by Shadow!Crewe on his 18th birthday, which was purposely invoked by Aelia For the Evulz.
A God Am I: Downplayed. Eon being a Latios is a species that are considered minor deities IRP, but he appears to have delusions of being on the same tier of power as legends like Groudon and Dialga, and demands that people worship him.
Absurd Altitude: During the Unown meeting, the group gets teleported into space, being saved from dying due to the Unown's power. They end up seeing the planet in its entirety before being teleported to the Sinjoh Ruins.
Achievements in Ignorance: For a long time, Daisy's Zoroark, Blacky, was able to use the abilities of the Pokémon he transformed into, even though said transformation is really just an illusion. Blacky seems to have caught on to this as his Illusion ability now works the way it's supposed to work.
Adaptation Expansion: The RP is mainly based on the universe of the main series games + spinoffs, but it also takes elements from the anime, manga, and even the TCG in the form of the Holon region, certain moves, and the existence of Delta Pokémon.
Adult Fear: Although Diane is not technically an adult, she is still horrified when Annie, her Head Pet Taillow, is almost killed by a giant Bouffalant.
Aerith and Bob: Both normal and plain unusual names are common. Ex. Mezzopiano Morendo and Jeff Firelight
Every being hypnotized into "silence", rendering him practically unable to do anything as it would make noise until the mind control wears off.
Palkia's dialogue after being restored from her petrification makes it clear that she was conscious the whole time. She doesn't seem too bothered by it, though, apart from having found being a statue to be really boring]
And Then What?: This trope is more or less what led Jane, Tagg, and Anom to become researchers. All three just didn't feel like doing nothing but battling for the rest of their lives.
Angel Unaware: Some of the legendaries can take the form of normal Pokémon or even humans to observe and deal with mortals. Ho-oh for instance has a tendency to masquerade as a Pidgey.
♨č▒⢫╠␣☣ł₤舸▟, or the Glitch Nidorino, is a representation of the fear of death that merely takes the appearance of the first being it encounters in the material world, in this case being Vinollo the Nidorino. Luckily unlike most other Glitches it's friendly if it's mission isn't to beat the fear of death into you.
The Invisible Shiny Bulbasaur that glitched up Kanto is another Glitch Pokémon.
Tagg considers a fair number of legendaries to be this trope due to their more eldritch qualities.
The main group, aka the J-Team, regularly coming up on top versus a number of dangerous opponents and containing some of the most skilled trainers in the RP's universe.
The PEFE Founders, particularly during their takedown of Pokefutures Inc.
The Extras, a group of vigilantes fighting off Cipher with minimal resources.
Badass Family: As found out in the Conquest Arc, several of the J-Team members are related to each other, not counting those who are already siblings.
Badass on Paper: Given how battles can be tackled from various angles besides strength or smarts, some Pokémon can end up becoming this. You wouldn't believe Dintel faced Lelouch and raised La Résistance to stop his invasion of Hoenn until you actually read it through.
Bag of Spilling: Tagg's Xatu takes his Unova badges shortly before the Unova-2 arc, forcing him to refight the Gym Leaders in order to get his badges back.
The Pokemon Trainers all end up turning into Pokemon when they go to the PMD universe.
During the OI, Fool (while possessed by Majora's Mask) turns three Pokémon poachers into shiny Pokémon.
Vyvyan the Magma Grunt starts unknowingly transforming into a Rayquaza due to having to keep Depthcharge and Buggle (clones of Kyogre and Groudon) under control. He is later kidnapped by Team Ozone, who speed up the process of his transformation.
Jane and her horde of Legendaries in the third arc.
Wolf and his Swoobat in the eleventh.
Tagg and a bunch of the other trainers teleporting down to Kanto to help Tracer and his Pokemon fight off a massive murder of Murkrow and their Honchkrow bosses.
Unite and Reshiram when they go first help with the evacuation of Goldenrod City, then stop an army at Rt. 32.
DS, the Lake Trio and Palkia during the final battle of the AU arc.
Lyuri showing up when Duke was having to fight Omega and Titan all on his own, allowing him to Mega Evolve and turn the tides.
Big Screwed-Up Family: The Cain-Davis family, of which Herbert and Psyche are probably the two most prominent members. Nearly every member of the extended family that's been shown onscreen is either evil, highly traumatised, just kind of a jerk, or some mixture of the three. The few decent ones almost always seem to end up dead or broken.
Big "WHAT?!": In the first Sinnoh Arc when Cresselia reveals that she is Darkrai's daughter.
Cipher serves as one for the entire RP in general, often acting through proxies instead of fighting the J-Team directly, having a hand in the backstories of several characters, and even created 'M which antagonized the J-Team during the Unova arc. For Orre they end up becoming the Big Bad of the arc.
OLD MAN's nemesis, the Magikarp Salesman, a powerful demon who doesn't really concern himself with the J-Team's antics at all.
The Seven Jerk Dragons serve as this for the PMD-R arc. While they don't make a direct appearance, their actions are directly responsible for the state of PMD-B when J-Team members visit it.
Bilingual Dialogue: Human and Pokémon characters talking to one another would count as this most of the time, with the humans speaking either English or other languages and the mons speaking Monese.
The fates of some of the J-Team members that survived the Draconic Uprising in PMD-B match this. The PEFE Founders for instance end up dying of old age unable to change things back, but they do end up laying the seeds to create a timeline fork and manage to raise families of their own.
The Fallout miniarc ends much like the original game, with the Super Mutants being defeated, but the Vault Dweller being cast out.
Wolf-B ends up saving AU!DS' life through sending a message through the Adamant Orb... at the cost of his own life.
The Orre arc ends with Cipher crushed (at least in Orre), but most of the Admins manage to escape justice (though not defeat), a lot of the J-Team members are left with issues, and Siren/Taylor ends up getting killed shortly after undergoing a Heel-Face Turn. On the other hand, Psyche does manage to conquer her own psychological issues...briefly.
During the AU arc, a bunch of the J-Team's mons board one of Lanius' slave ships and manage to rescue the slaves aboard.
A very well-organized one occurs in AU!Goldenrod when the Pokémon there have to try and counter the initial Draconic offensive, including Ariados-silk cable anchors and feline mons effortlessly climbing them up to the airships above the city.
When DS first meets Chase the Pidove, he mentions that his wing was injured by a Purrloin. DS eventually catches said Purrloin.
DS has Brain Bleach in her backpack. This is referenced and used many times.
Chase meets the flock of Pidove that left him behind in Nuvema town after joining the group.
Briar Rose learns how to bring objects from the Dream World back with her to the real world, and intends to use this information to bring back some berries she had planted in the Dream World. Next time DS sends Briar Rose out of her ball, she has the berries with her.
Brief Accent Imitation: Jane donned a Southern Accent near the beginning. It went away after a while, though it still slips through on occasion.
Broad Strokes: Since WAAPT evolved from a Forum Game with no real continuity, the defeats of Missingno and 'M are considered canon, but not everything that happened in the interim.
Call a Rabbit a "Smeerp": Zig-zagged. Most regular animals don't exist, and sometimes an animal is mentioned and the trainers won't know what that is. Other times, they refer to certain Pokémon as the animal they are based off of.
Carnivore Confusion: Yes, every Pokemon in the setting is perfectly sapient, and yes, the predatory ones will kill for their food. The prevailing view amongst predators when hunting is to mainly aim for jerks and not to revel in the kill.
An overarching one appears to be that people are people, even when they're not human. Humans and Pokémon are shown in many instances to be Not So Different from one another in both positive and negative aspects.
Conservation of Ninjutsu: Our heroes regularly end up blasting or beating their way past veritable hordes of Pokemon, but can be given a fair amount of trouble when fighting one on one.
Continuity Lockout: It's really hard to jump in during an arc because of the heavy continuity. This hasn't stopped some people from jumping in anyway and then realizing there's too much stuff going on that they don't know about to actually keep playing. This hasn't stopped a few dedicated players from joining the group.
The Alakagross civilization had quite a few, which the dragons in the AU base their airships on.
Team Glacier has an airship piloted by Shadow.
The J-Team in general acquires a damaged Illusion Project airship and makes it their own, which becomes even cooler once it's upgraded at PEFE HQ.
Cool and Unusual Punishment: The judgments handed out by the Cubone tribe during Tangent, Tagg, Tracer, and their Pokemon's "Trial by Bonemerang". Examples include having to give all the kids in the tribe a ride (Tagg's Garchomp) and being unable to use Yache Berries for a month. (Gaia, Tagg's Torterra.)
Cybernetics Eat Your Soul: They did in the case of the main opponents Tagg and some of the others faced off against during the PEFExp miniarc, cybernetic Pokémon that had been lobotomized into fighting machines by Pokefutures.
WAAPT in general deals with heavy subjects such as racism, imperialism, and gender identity, and villains like Cipher are far more explicitly playing for keeps.
The alternate timeline is much darker than the OU, with first Napoleon cutting a bloody swath across Unova and the Seven Jerk Dragons in RtAU attempting what amounts to PG-rated genocide on the human race.
Tagg's solo adventures tend to have a darker undercurrent than the main RP since he tends to fight groups like the Unity and Cipher who are far more ruthless than run of the mill villains.
The Orre arc was the darkest arc the RP has seen since the AU, with quite a few deaths, mass killings, trauma for nearly everyone involved, and the full ruthlessness of Cipher falling on the heads of a J-Team unprepared to handle it.
Missingno and 'M end up being destroyed in every verse due to the OU J-Team defeating them.
What happens to Napoleon in the AU after the souls of the Midori Room mons maul his soul, tearing it to shreds. Though Snowball does end up using said shreds to create Icelus, Napoleon himself is gone.
Death Is Cheap: When Gamer's Serperior was killed by David, he came back to life as a Duskull. Also, Daisy's Charizard is killed by a madman behind the madness in Canalave City. It then re-appears the next day as a Gastly.
Quest Island, which is filled with dangerous Pokémon like Tyranitar and Skarmory, as well as having a easily awakened volcano. The Cubone tribe patrols in other regions are done by Marowak, and infant and child mortality is at a very high rate.
Other examples include post-Distortion Sinnoh in the AU, and both the AU and OT Giant Chasm.
Assumed to be done by Missingno in an attack on Canalave in the original Sinnoh Arc. Turns out it was just a Gastly, though. Prior to the first PMD Arc, though, the real Missingno pulls this on Palkia.
It also happened a lot during the Unova arc. The victims included Steven Stone, Iris, Clay, Alder, and Jane.
Happens to Cynthia near the end of the PMD arc, and to Jane, Wolf and Pentigan during the battle against 'M and Team Plasma at the Pokémon League.
DS is seemingly killed by Primal Dialga in a flashback, but unbeknownst to everyone, Dialga was able to resist Cyrus' orders and instead sent DS to the dimension in which the legendaries had been imprisoned.
Straw has experienced this enough times that he is pretty much unfazed by it.
Die or Fly: Auric and Obscuric abilities tend to be learned very quickly by those stuck in life and death situations.
Doorstopper: As of May 12, 2014 the RP is about 14,892 pages and counting, and text-only versions of single forum pages on the main thread alone can be in the range of 5-8 pages. A conservative estimate of the amount of printed pages would be about 105,000 pages and counting.
Don't Go in the Woods: Tagg lives next door to an area known as the Sea of Trees, which happens to be based on Aokigahara, the infamous suicide forest, and possesses a similar reputation. It's infested with hostile Ghost types and the souls of those who have died in the forest.
Umbra had the ability to banish people to the Distortion World back when he was the Ghost Lord of Spectra.
Tagg gets rid of the Sinnoh Family of Blood branch by having Groudon take them...somewhere else.
The Dragonslayer: Inka somehow gets this fame after curbstomping Lance's haxxest Dragonites (you know the ones) in backstory. However, by the time of the Draconic Uprising in the AU timeline, she is forced to live up to the title.
The Dreaded: A number of the Trainers, including Luke, Tracer, and Tagg, gain this status during the AU arc after curb stomping their way past hordes of Scolemis grunts.
Dramedy: The story is mostly humorous, though it can take some dark turns.
Dream Land: The Pokemon Dream World, a collective unconsciousness made from every Pokémon there ever was.
The trainers do this to infiltrate the Altru Tower in Almia.
Tagg and the Vault Dweller end up doing it in PMD-B Angela in order to infiltrate the Cathedral.
Dropped a Bridge on Him: Upon finding a treasure room which turned out to be Larva and Metentis' summer house, Brudy was abruptly eaten by Larva the Cofagrigus after Metentis the Dusclops told her she couldn't have any servants.
Dying Declaration of Love: Mira to Artemis in the AU arc, after the former is fatally injured after receiving a stab wound meant for the latter.
Dysfunction Junction: A lot of the trainers have serious issues of some kind. Some examples include:
Tagg, who has social issues, PTSD as a result of his experiences during the AU arc if not long before, and has admitted to DS that he only really feels comfortable In Harm's Way.
Lyuri Riese, whose parents died in a cave-in thanks to an Earthquake caused by Riku the Sandslash and were separated for several years. And then Orre happened. In the AU Lyuri is the last member of her family since Sakura ended up dying too, leaving her a Broken Bird. This does not apply to her sister, Sakura Riese, though, as even though she shares the backstory, she doesn't have any lasting issues other than feeling guilt over the death of her parents.
Herbert, whose father is a Team Galactic commander who was still a better parent to him than his mother, who acted as if he didn't exist.
Jacob, who was orphaned when his parents were murdered and had his girlfriend killed by a Scizor. He also happens to be a bit unstable.
The Amarin family, consisting of Alli, a girl who seems relatively normal, but hides the trauma of losing her mother when she was just eight years old; Eskay/Sarah, her older brother/sister who saw the aforementioned death firsthand as well as almost dying the same way himself six years later, along with having accidentally murdered a Cipher Peon in a fit of rage despite having promised to never kill anyone ever, resulting in full-blown PTSD (which is only amplified by his empathic powers); and Ivy/Ellen, the dead mother in question who came back as an amnesiac Delta Golett and only regained her memory by witnessing the aforementioned attempted murder of her son.
Wolf, who was 'M's thrall for nearly ten years prior to the beginning of the RP, though he's managed to get past that.
Psyche, whose father was abusive and disowned her after she got mauled by Scrafty, leading to her Cynicism Catalyst.
Alyssa, another PTSD victim whose parents were killed by a fire, leaving her orphaned and lost in the wilderness with no social skills, along with leaving her with a haunting phobia of fire.
Crewe, who apart from being actually a Sneasel in human form, has a lot of issues regarding so many of her mons leaving or dying on her as well as possible PTSD from both that getting shadowed and nearly killing Straw in Orre.
Early Installment Weirdness: The earliest arcs (Sinnoh through Unova) are far different from the RP today, due to it being originally a forum game with no real continuity that evolved into an RP. Word of God says that was due to Missingno and 'M's mere existence making the world of WAAPT a far stranger place than it is in future arcs in-universe.
The AU arc. Its plot reaches numerous dark and overwhelming moments before its ultimate (and satisfying) resolution.
Sakura lost her parents and had her sister go missing, she spent a good four years looking for her and feeling very guilty about everything that happened, she eventually finds her, they're in good terms with each other, and she even got a boyfriend soon after, while she does occasionally have more problems, they're either minor ones or don't take as much time to be solved.
Earth Is a Battlefield: Not a single region on the planet manages to escape war during the Draconic Uprising in the AU.
The only members of the J-Team that seem particularly bothered about Umbra's past as an Evil Overlord are Herbert and Sakura. It helps that it took place 600 years ago and Umbra isn't the same person he was back then.
Likewise, the only members of the J-Team who don't quickly forgive Tagg for slaughtering dozens of Cipher Peons are Herbert, Mezzo, and Sarah. And the only member of the team who still holds a grudge against Lyuri for her crimes as Alexia is Herbert. Sensing a trend here?
The Anomaly aka Missingno and 'M, biological supercomputers whose mere presence warps reality.
The imprisoned being found in the deepest recesses of the Blacklight Caverns in the Orre Badlands in Dune's backstory, which he only barely escaped from, at the cost of his mind being scarred and incapable of being touched by any kind of telepathy. Known as the "Criminal", due to the runes in hundreds of languages stating the word around its prison.
"The Duke" and "The Prince", two possessing spirit things, the first in Pi's head, the second in the head of the villain Mortimer.
The dimension where the heroes took on Missingno for the first and last times.
Glitch City, 'M's home dimension.
Some of the Mindscapes
Elseworld: Many, but the two most often seen are the AU created from Cyrus' time tampering, and the Another!Verse (Based on The World Ends With You's Another Day mode), a Lighter and Softer version of WAAPT.
Enemy Within: The boss of each trainer's mindscape during the Mindscape Miniarc tends to be their inner dark side.
Ensemble Cast: While certain characters can gain more prominence than others depending on the arc, the RP lacks a defined main character.
The Lieutenant dies from taking an Earthquake to the head from Emperor!Archeops in Tracer's body and ends up starting to liquefy like his counterpart from Fallout before getting telekinetically hurled into a vaporizing forcefield.
Jacob ends up stabbing a Scizor with a sword after it kills his girlfriend in a flashback. Complete with the sound of the exoskeleton shattering!
Ivy/Ellen Amarin's death involved getting stabbed by a Toxicroak, and bleeding out along with the deadly poison right in front of her own son. Eskay almost receives the same fate, but is quickly saved by Ellen herself, Back from the Dead as Femata the Delta Golurk.
Ninetails dies from Tagg disemboweling her after Ammy and Herbert slice off all of her tails.
The Litwick and Elgyem members of the Celestial Tower do not get along.
Delta Pokémon are often seen as freaks by non-mutated mons.
Due to the Seven Jerk Dragons's part in trying to usurp the legendaries and more or less genociding humanity in the PMD-B timeline, Dragon types in general are often treated as second class citizens outside of Hoenn, which is more or less persona non grata due to other mons seeing it as merely a continuation of the Seven Jerk Dragons's rule due to a quirk of the mon bombs rendering most transfigured humans Dragon types.
Faithful the Salamence was originally prejudiced against non-dragons.
Cubone line members in general tend to be wary of non-Cubone, referring to them as "fiends" due to the fact that most other species prey on them.
Axew and Deino line members in the wild will kill one another on sight, leading to Tagg's Hydreigon having a prejudice against Vektor the Delta Fraxure, as well as Axew line members in general.
Gyru the Bronzong despises all organic mons as well as humans, considering them beneath him.
The Ghouls of PMD-B Angela tend to dislike all non-Ghost types.
In the PMD-B timeline and within the Return to AU arc, the draconic forces heavily discriminate(d) against non-dragons in their ranks and in general, with the goal of exalting themselves above humans and other mons in general as the rulers of a mon-only world.
The group as a whole would also count as their friendship deepened through their mutual experiences fighting evil.
Cinder and Lake in the AU go this way, as they realize they share having gone through many of the events that marked their lives with their Trainer, they just happen to see it differently. Somewhat lampshaded when they remember their challenges of Whitney.
Tagg and Herbert start being more friendly towards one another as they travel through Ransei with Ammy. Unfortunately undone in the Orre arc.
Fisher Kingdom: Type 2. The two PMD universes will turn any human who enters them into a Pokémon of some kind.
Five-Man Band: In the beginning it worked like this, but after the group got a lot more members it became closer to The Team. The breakdown pre-Oblivia worked like this:
Fixed Relative Strength: While as a whole the group is made up of powerful trainers, with even the weaker members often having at least one league under their belt, some are indeed just leagues ahead of others.
A sweeter form of it though with the Breather Arc foreshadowings during the AU.
Four Lines, All Waiting: Aside from the main plot of an arc or arcs, there can also be numerous subplots, including ones taking place far from the region the bulk of the J-Team happens to be in at the time.
Happened three times from Sinnoh to Unova-1, first with Jane and Palkia, the second time with DS and Artemis and the third with Daisy and Pink. A weird variation of this also seemed to happen between Jane and Entei.
Happens yet again with Anom and Wolf, due to a Manaphy. Unlike the other examples, it's played as a more serious major plot point rather than a brief joke, and lasted for pretty much the whole Oblivia arc.
This later happened in Kalos when a particularly "playful" Obscuric being decided to swap Mezzo and Eskay's minds. This ended up causing a small amount of chaos, especially when the fix turned out to be a kiss.
Deziree, Psyche, and Pentigan end up switching bodies for a brief period during the Fiore portion of Ranger-2.
Free-Range Children: Pretty much all of the characters that are or were minors starting out would count as this. Bonus points go to Amber and Remy for not even being in the double digits when they started.
Friend or Idol Decision: During the finale of the Orre arc, Tagg finds himself having to choose between killing Tokarev, or rescuing DS, who is in danger of falling to her death into a pool of lava. He chooses to save DS, in the process realizing how much his desire for revenge against Cipher had consumed him as he actually had to think about whether to save one of his closest friends or not.
Gentle Giant: Many large and imposing Pokémon are like this.
Gondor Calls for Aid: Tangent and Tagg's Xatu manage to gather a large amount of peoplemons that the J-Team has helped in order to help prevent Cipher from taking Gateon Port at the climax of the Orre arc.
Gory Discretion Shot: We don't see Tagg murdering dozens of Cipher Peons as a threat toward the Admins of Cipher and as revenge for what the organization did to him about six years before the start of the RP during the Orre arc plus what they did during the arc, but we do see its aftermath.
Happens when the wild Pokémon around the Orange Islands talk about Algira after she becomes a wanted mon for eating some of the bug Pokémon on the islands. Algira goes from just another predator to a monstrous demon hellbent on devouring every Bug Pokemon on the islands.
Happens again when Latias begins searching for Pentigan's lost Gender Bender amulet so he, Anom and Fool can be returned to normal. This eventually leads to the wild Pokémon searching for a non-existant Soul Dew because they think Latias will reward them with a lifetime's supply of Oran Berries if they can help her find it.
Anyone who manages to transform into a Pokemon has their DNA slightly changed to become part Pokémon once they turn back. It has not been directly confirmed but it is likely the same for any Pokémon that transforms into a human.
April Fools 2013 had this happen to Sakura and Lyuri, mirroring the Pokémon RéBURST transformations, they became an Arcanine and a Lucario, respectively.
Gyru, a mechanical Pokémon with a robotic superiority complex, is turned thus becoming an organic, inferior being (to add salt to the wound, it has to eat to be cured).
Hard Light: Moves like Reflect and Barrier can be made to work like this. Sol uses them to redirect light, reroute fluids and attacks, and shelter Trainers during battle. Auric constructs work in a similar manner.
Magic Guard renders Selene the Clefable immune to poison darts.
Safeguard can guard against toxic gases and temperature extremes as well as status moves.
The often overlooked move Round was used at Tagg's Vanilluxe's suggestion to disorient a Soulless T-Rex in AU!Sinnoh.
Heroic BSOD: Several characters have gone through this in the past.
Hero Insurance: Averted, the trainers end up getting banned from a number of Hoennese hotels due to their destructive antics, or to be more exact, their Pokemon's antics.
Heroic Sacrifice: During the final battle against 'M, Anom (who had his DNA become unstable after the events at Twist mountain) tricks 'M into absorbing him, which destroys 'M's anti-legendary shield and allows the legendary Pokémon to join the battle and finish of 'M once and for all. Anom ended up Deader than Dead, until the legendary Pokémon figured out how to bring him back after a week.
The legendaries accidentally destroying the Sky Fortress didn't sit well with its wild Pokemon population.
The main group gets this so badly at one point that Pokepan hotels start denying them service, starting with Hoenn.
Humanlike Animal Aging: Zigzagged, while most species of Pokémon can live at least as long as humans, and others live shorter or even longer lives (With ghosts and inorganic mons being immune to death by old age), Pokémon generally physically and mentally mature at an accelerated rate compared to humans.
Missingno, also known as The Cinnabar Anomaly, The Anomaly, He Who Must Not Be Numbered, It, The Unnumbered One.
AU!Alduin, the World Eater, Kingsbane, and God of Destruction, much like his namesake.
Lugia, also known as the Great Dragon, the Guardian of the Sea, the Leviathan, Singer in Darkness, He of the Silver Wings, Soulstorm, the Fulcrum, the White Wanderer, the Living Moonlight, the Prince of the Sea, and The Titan of the Abyss.
Dialga, also known as the Archwyrm, the Chronosaur, Father Time, King over the Mountain, Master of the Fates, Doom, and Lord of Time.
Palkia, also known as Epoch, the Spatiosaur, Mother Earth, Queen Regnant of the Eyes, Maîtresse sur les routes* Mistress of the Roads, and Birth.
Arceus, referred to as the Alpha and the Many Armed One, among other names.
Teresa and Jacob, after the latter was hit by a wild Pokémon's Toxic. He does end up getting cured though.
AU!Tagg has one of these in the PMD-B timeline, which likely influenced his decision to entomb himself in his vault with the Adamant Orb.
Infant Immortality: Averted, kids can get seriously hurt and in some cases have even died IRP. Examples include:
Forte ends up getting his arm broken by an Armortomb and in the AU is killed by a Bisharp.
Fortis dying in the AU and getting reincarnated as a Drifloon.
When Kat and Rising Star visit the Route 9 Tribe's graveyard, the grave of a young Cubone can be seen.
Tagg offhandedly mentions that the mortality rate for young Cubone on Quest Island is extremely high.
Lanius' forces strung up children on crosses as well.
Innocuously Important Episode: The events of Twist Mountain are mostly just a series of mind screws, but it does set up a few plot points. Including one that ends up being the key to taking down 'M's anti-legendary shield.
Luke and Reshiram. It doesn't work at first, but they change their minds quickly and end up together anyway. Which is later countered with Jane and Zekrom. Until they break up once the two Tao Dragons recognize their feelings for one another.
Algira, Silent's Masquerain, having a crush on Tagg, much to his chagrin. She falls for Helios, Tagg's Volcarona, when she gets over him, though they do share Egg Groups.
Implied for Clover and Glaze (Kim's Lopunny and Minun).
Sierra and Vyvyan, after Vyvyan's transformation into a Rayquaza. At least he does get to keep one of the Pokémon-to-human armbands so he can turn back and forth between his Rayquaza and human forms as he wishes.
Umbra with Ammy, a Volcarona who uses an armband to remain in human form most of the time.
Lyuri and Duke, a Lucario, in a similar fashion to Umbra and Ammy above.
Kisune and Ren. With Kitsune, a larger than average Ninetales, being in love with Ren. Ren reciprocates her feelings when she wears the Borked Armband for a couple of days.
It Sucks to Be the Chosen One: Just ask Maekrite. Got Volunteered to attach to a Trainer despite his mother raising him for having a full, wild life? Check. Having to leave behind his mate before they had the chance to share a breeding season? Check. Can return home for a visit once every six months if he's lucky? Check. Can barely see her during those visits? Check. Having to take up the same mantle in an alternate timeline despite extensive Screening Of The Call? Check. Sanctioned by Ho-Oh to do the same things Only More So - and essentially for life? Check.
I Will Find You: Wolf and DS make this promise to each other just before Dialga alters the timeline.
Jerkass: Some of the pokemon are total jerks. Examples of which include:
Courtney, Tracer's Unfezant, who tends to be a mostly unpleasant individual.
Fade, Every's former Drifblim, who gets pleasure out of mean-spirited pranks in order to feed.
Gyru, Every's former Bronzong, who happens to be an inorganic supremacist on top of that.
Zack, Lyuri's Floatzel, constantly bullying Riku, even talking about the cave-in he accidentally did out loud when he was asked about it, and just being a Jerkass in general, he does get some payback from his antics sometimes though, he has shown to have a Hidden Heart of Gold or close to it when he helped Riku out of his short BSOD after a car crash, but is still a prick most of the time.
Luana's Marowak, who once called Limna (A Blaziken/Feraligatr chimera) a freak among other actions.
Eon, one of the Seven Jerk Dragons, definitely earns the title by being a arrogant, racist tool.
Journey to the Center of the Mind: The basis of the entire mindscape miniarc, which involved a good portion of the group exploring eachother's mental worlds after Crewe is revealed to be a Sneasel transfigured into a human by a Mew.
At the end of the Unova arc, Anom is entrusted with a Manaphy egg by Cynthia, and has to make sure it safely makes it back to Oblivia. Anom is strictly told not to tell anyone. However, this trope doesn't come into play until the Oblivia arc when Anom ends up being Heart Swapped with Wolf, and the Pokémon Pinchers capture and escape with the Manaphy, leaving Anom and Wolf stuck in each other's bodies.
They initially try to keep it a secret and pretend to be each other, but things get complicated fast. Eventually, the tension within the group gets so bad, the secret gets shattered.
Luke, You Are My Father: Cresselia is Darkrai's daughter... or at least she claimed to be. Seeing as a book in a library in the Dream World refers to Darkrai as Cresselia's brother, this may not be true.
Magical Computer: It could be argued that Super Nerd's Hoodie Computer is this, as it seems to be able to do anything within the laws of cyberspace.
Magitek: While not outright stated, the armbands are implied to be from an unknown ancient civilization.
Mayfly-December Friendship: Tagg (Normal human lifespan) and Umbra (immortal), and pretty much all of Umbra's friends for that matter save for Lina who's also immortal.
Meaningful Echo: When Chase as a Pidove rescues Artemis from a Scolipede, he comments: "She may be a jerk, but she's still my team mate!" Later on, after both have evolved and Chase Took a Level in Jerkass, Artemis ends up saving him from a Beartic. Afterwards she comments "You may have been a jerk, but you're still my team mate."
The PEFE (the Fanon Pokédex organization) appears to be like this, Type 2 ("smaller, centralized [...] in something... dangerous"). Whether they are benign or not is to debate, considering its superiors hijack fangirls in a container to use them in experiments with Shinx. Then again those being fangirls, make of that what you will. This was due to the fact that they ended up taking over the assets of an actual Mega Corp, Pokefutures, Inc.
In the AU the Pokepanese military in Kanto more or less held in Vermilion and let Lanius' forces run roughshod over Celadon and Saffron after they attacked, though this changed once Lt. Surge came back and rallied them into fighting back.
They also proved mostly useless in the initial portion of the RtAU arc, though this was because the dragons were using Lost Technology they were ill prepared for, and monification created mass chaos. After that, however, quite a few ended up making the backbone of guerrilla movements.
Mind Rape: In WAAPT it's mainly of the psychic assault variety, with the result of an unrestrained assault being brain death.
[[The first Glitch Area in Canalave. To elaborate: Jane's and Gamer's pokemon are genderbent, Mewtwo is in a woman's one-piece bathing suit and reading the instruction manual to Pokemon Platinum, Gamer has turned into a Snivy, Jane and Palkia have switched bodies, and the Regis are all wearing hats for those who are curious, start here.]]
The ending to Goggles' backstory. Did any of it actually happen, or was it just Goggles' daydream? What was up with the Maractus? And who was doing the voiceover at the end?
Twist Mountain in the first Unova Arc was another Glitch Area with similar results.
If an armbanded human is caught while in Pokémon form, the Vow takes precedence and the human is forced to stay as a mon unless they're released. (The armband can be taken off, but they won't shift back to their original form.) However, putting on a Pokémon to human armband can work around that restriction.
The mon bombs used by the Seven Jerk Dragons work under similar principles, including the Pokémon to human armband loophole.
Tagg's adventures during the OI arc had elements of this as he was doing a Super Mario Sunshine themed adventure while dealing with the aftermath of his actions during the AU arc.
Umbra's humorous dream where he's a pimp and Ammy and Lina are two of his "workers" turns into a nightmare where Duolis shows up and reams him for first pimping them out, and then for his past as the Ghost Lord of Spectra.
There is at least one person from every main series region to date inside the group as of Gen VI, save for Anom, Daisy, and Kim, who were born in Oblivia, Orre, and Almia respectively. Other exceptions include Umbra who was born on Shadedrake Island off Hoenn, and Lina who was born in Dragnor, Ransei.
Team Skyclaw goes to solve the mystery of some disappearing mons in PMD-A, only to find out that the reason is not some monster, and certainly not the seemingly obvious Gulpin and Swalot family they meet, but some rogue mons.
Also within PMD-A, DS nearly got killed after discovering a fake rescue team that was going around eating "civilized" mons, basically making them the equivalent of cannibalistic serial killers.
The Adamant Orb in this continuity grants time control powers on top of its canon abilities of powering up and summoning Dialga. What does Tagg tend to most often use it for? Getting a full night's sleep in only a few minutes by exploiting its Year Inside, Hour Outside time dilation effect as well as getting rid of jet lag.
The usage of the Hammerspace backpacks as tents and sleeping bags due to their infinite volume.
Pianis uses Sparkplug the Frost Rotom as a refrigerator.
During a party for the proto J-Team in Unova, Heatran's back is used as a grill.
Discussed by Tagg and Fool when they share their mutual experiences as a field researcher and someone who was Raised By Animals and is often invoked in both of their thoughts about the subject.
When Helios rescues Algira in the alternate timeline, by knocking the Swellow hunting her and her friends into a lake, they chatter happily while the Swellow is suggested to be being eaten in the background. Helios invokes the trope by name.
Kirk learns this firsthand when he ends up in Kalos and gets his meal stolen by a Hydreigon, who mocks him about being a weak "pet" unfit for wild life.
Neglectful Precursors: Tens if not hundreds of millenia before the rise of humanity, the dominant species were the Metagross and Alakazam, who created rival civilizations. Following their activation of the Mt. Pyre supervolcano, which the weather trio sacrificed their lives to prevent from fully erupting, the legendaries wiped both civilizations from the face of the earth for their arrogance. Chrome, Lina's Metagross, happens to be a survivor of the original Metagross civilization.
New Eden: During the course of Team Earthbound, Nova, and other's adventures in PMD-B, they find that many of the old cities have gotten a new coating of green. Azalea for instance was completely swallowed by Ilex Forest.
DS unknowingly made a few comments that inspired the Impossible Thief Emolga to steal Tagg's cynical side. As a result, Nihilist!Tagg was unleashed, and some of the trainers had to fight for their lives while DS went off to find the Emolga and get Tagg's cynical side back so he could be returned to normal.
Tagg ends up starting the Keystone arc by taking Annoski's Keystone to the spot it needs to be for him to revive.
During PMD-B Tagg's group allowing the last two Super Mutants to get away doomed Necropolis by having the Master send his army to destroy the place in reprisal.
Fool goes through a rather freaky one during the AU Arc in which she sees herself (The one she identifies as "Sol") using the corpses of Pokemon that she murdered as marionette puppets. A Shout-Out to a very similar scene in Felidae.
Happens to Sakura not too long after her debut, she mentions that it happens frequently, but they stopped once she found Lyuri.
Straw goes through these at least somewhat often, such as being stabbed by Jab and dreaming Crewe died and he was only finding this out when he was married to Elise.
Tagg has one following the Orre arc after drinking himself unconscious at Kat's wedding.
Sarah has had frequent nightmares since her trauma in Holon, but a particularly interesting variation occurred when she experienced Sakura and Blitz's trip into her Mindscape through the eyes of the aspect that was actively trying to kill them.
No Dead Body Poops: Averted in the case of a hunted Rapidash, and is actually discussed at an earlier point.
Noodle Incident: Several of these have been brought up, and some of the things that are mentioned to happen off-screen also qualify for this trope.
After returning to their human forms after defeating Missingno, the trainers discovered they still had the ability to understand Pokémon speech.
Some of them do it intentionally by using the armbands just because of said ability.
Lyuri still has the ability to use Aura after being turned into a Lucario hybrid, despite being turned back to normal, and before her, Kim and Lily after being turned into a Riolu and Mienfoo respectively.
Nothing Is the Same Anymore: The AU arc caused some radical changes in the RP both in-universe and in the meta, to the point that to the point that it's referred to as the Upheaval Saga.
Not-So-Harmless Villain: You'd think that two Go-Rock Squad Admins would be easy for our heroes to defeat. You thought wrong. The two of them gave our heroes quite a run for their money before Casval and Pentigan's actions helped turn the tide by temporarily fixing Gordor's pipe organ Power Styler and breaking their control over their hordes of Tyranitar and Metagross, as well as their secondary instruments getting stolen by Librarian's Hitmonchan.
The group fly off to Sandgem town to ask Professor Rowan some questions, but after the others have already left, Daisy remembers that she doesn't have a flying Pokemon with her. When the others arrive at the lab, Daisy suddenly shows up with no explaination of how she got there. No one seems to notice.
Frequently happens when a character is inactive thanks to the player being busy or something along these lines.
Oh Crap! There Are Fanfics of Us...: It happened first around the GC Arc when the J-Team found out about the fanbase they'd amassed due to slaying Missingno and 'M, and it still happens occasionally when newer members learn about the fanbase.
Whenever there's a "Freaky Friday" Flip, players tend to switch their avatars to that of the normal player of that character.
The use of music IRP to affect the mood of posts.
The Terrifying Presence Auric power is signified by the use of eviltext IRP.
Heart of Gold super empathy is signified by the use of gold text.
Thoughts, whether telepathic or otherwise, are often signified by the use of italics.
Brackets are used to signify Monese, except in the PMD universes where everyone speaks it, save for PMD-B when the brackets come back for interaction with humans.
Glitchmons tend to use an intentionally glitchy font when speaking.
Pals with Jesus: The group is, as a whole, good friends with Palkia and other legendary Pokémon due to inadvertent events in the past.
Paper-Thin Disguise: Lenore (Fool's Hydreigon) and Ammy use these to get their own Trainer's Licenses - they wore fake moustaches and trenchcoats. Lenore's case is more notable, because while Ammy was wearing a Pokemon-to-Human armband, Lenore wore the disguise as a Hydreigon.
Pen Name: "MidnightSun197", a writer of romantic in-universe fanfic, is actually Sunny, Mezzo's Umbreon.
Pensieve Flashback: Psychics can use their powers to allow people and Pokémon within a certain radius to see the memories of themselves and others as observers. Aura can be kneaded into the projection to get around the difficulties most Dark types have with this.
Place of Power: The Aura Nexuses around the world, which give increased powers to those in the Auric Quartet (Aura, Psychic Powers, Ghost Obscura, Dark Obscura).
AU: Umbra getting sealed in an orb when he was the Ghost Lord, Hoenn getting flooded, Sinnoh suffering the Distortion, and Anom's Scolipede and Artemis taking over Unova.
PMD-B: The dragons succeeding in turning 99% of humanity into Pokémon.
Otherverse: The earliest known important divergence is Grings Kodai using Azalea instead of Crown City for his Celebi plot.
Poor Communication Kills: Caitlin's Sigilyph notices Alder's eyes glowing briefly while he speaks to Caitlin, who is starting to lose control of her psychic powers because of 'M. Realizing that Alder may be controlled by 'M, Sigilyph tries to warn Caitlin's other Pokémon. Unfortunately, said Sigilyph happens to be The Unintelligible.
Portal Network: The Entralink in this verse is capable of facilitating multidimensional travel with its counterparts in other universes, though it can be unreliable in this regard.
The Power of Friendship: DS invokes this in order to use the Lustrous Orb to revive the petrified Palkia during the AU arc.
The Power of Love: It's heavily implied that Wolf's feelings for DS are what allowed him to come back to life.
Pronoun Trouble: Virizion. Usually people just go with whatever gendered pronoun gets used first, but so far Virizion is the only one who everyone has pronoun trouble with, eventually sparking a debate between Anom and Jane.
The main point of the Abbyfall quest in PMD-B was to prevent the Bay region of Hoenn from exploding into war once again.
Tagg's group in PMD-B hands over the letter stating the Hoennese royal family's claim to the Pokepanese throne to the Hoennese emperor in order to head off any wars of regional supremacy by powers who would view it as a threat.
The Quisling: In the RtAU arc, Vallok gets some draconic humons to betray their species in return for better treatment, including Benjamin old classmate Reggie, who now goes by Julkriid.
Ready for Lovemaking: At some point and while their adopted daughter is busy somewhere else, Harriet the female Honchkrow tidies the nest and leaves just the right amount of space besides her for Copahue the male Fearow to fit in.
Real Time: For the most part, a day IRL equals a day IRP, which means that characters age as the RP goes on. For example, Tagg aging from 19 to 22 from 2011 to 2013.
Reality Ensues: Despite the more outlandish aspects of the RP, realism can indeed rear its head:
The PEFE Founders took down the corrupt corporation Pokéfutures Inc., who also happened to be the lynchpin of Angela's economy. This resulted in the Angelan economy going into freefall, and had the Founders not took the deal to take all their asset they would've all ended up in prison.
Raise loads of sapient beings for use in competition and basically rejecting most for one or two perfect mons like in the games? Be prepared for a lot of issues regarding self-worth, if they don't outright hate your guts.
Verax may have done a Heel-Face Turn, but that doesn't mean the J-Team members who he's tried to kill before are going to like having him around.
Daisy and Pentigan got together due to their adventures fighting Glitch Pokémon, but once that was over, they found that apart from a shared horrific experience they didn't really have anything else in common and broke up.
The J-Team causing property damage to the places they stayed at caused many hotels to ban them from staying there.
Psychological issues take time to fix and may never fully go away.
During the Hoenn arc Tagg decides to have his mons destroy a perfectly legal Neo-Magma machine to stop them from destroying a beach and is forced to retreat by them calling the cops as that's vandalism.
Even though DS was seemingly killed in a flashback during the AU arc, it turns out she was merely imprisoned in the dimension where most of the legendary Pokémon had been imprisoned.
Also somewhat played with when DS and the Lake Trio discover that Palkia was basically petrified all along.
Straw is believed to have died when a ship sinks in the Whirl Islands, but it turns out that he was very much alive.
Research, Inc.: The type of Mega Corp. the PEFE happens to be, focused mainly on the betterment of Pokémon and humans alike.
Retcon: There have been several of these, not always done on purpose.
Ret Gone: Ribbons the Gothitelle, and several other Pokémon that were born because of the trainers vanish when the timeline was altered. However, Helios and Limna managed to avoid this fate thanks to the power of the Adamant Orb making them time paradoxes.
Rules Lawyer: The dragons decide to turn humans into Pokémon because if they tried to simply outright slaughter them the legendaries would eliminate them like they did the Alakagross due to the rules of the Vow dictating conduct between humans and Pokémon.
Tagg's Zweilous and later Hydreigon wanting to eat someone or something.
People forgetting about Slouch.
MGMT (Fool's Eelektross) being referred to as an overpowered jukebox.
AU!Chase telling the Resistance something involving hard work, and a random crowd of Resistance members responding with "Yay".
Any delays in Pentigan responding to posts when there isn't anyone else around is caused by rogue agents of Scolipede. Even when not in the AU arc.
Forte being described as whiny.
Maggie getting her pants removed in some fashion.
Doopliss trolling Straw and/or Crewe.
Straw dying and coming back to life.
Ever having to do some sort of odd job.
Vierr's weird dreams at the start of Ranger-2.
Once Crewe gains the ability to teleport, "-there is now a Sneasel here-" becomes one.
The WAAPT chatroom has some of these as well:
When in doubt, blame Cyrus
DAMN IT, NAPOLEON
Eskay getting disconnected, then saying "Dammit iPod" upon return
Oran Berries fix everything.
[Someone] x [Someone else] OTP!
Anom turning into another person.
Silent['s mon] kicks a random pebble.
Every setting an anonymous login on fire, only for it to turn out to be another player, especially Star.
Chatroom Gamer is OP!
When Crewe gets tired, expect bagels. Lots of bagels.
STRAYLOOOOOOOR (or STRAYLOR OTP), regarding the Straw x Taylor ship and it's abrupt sinking.
Sand in My Eyes: Before she began opening up to the rest of the group, DS had at least two instances of this. There has probably been other instances of this trope from some of the other characters as well.
The Savage South: Quest Island of the greater Sevii Islands chain is a sparsely inhabited, unforgiving place filled with dangerous Pokmeon such as Tyranitar and Skarmory.
Wolf falls in love with DS, but she doesn't know that and only considers him as a friend at first. Later, Wolf confesses his feelings for DS and kisses her (after turning into a girl). They eventually get together after Wolf changes back.
Rebecca the Serperior so far has two suitors; Goggles the Krookodile and Blacky the Zoroark. Though her true suitor ends up being Antoine the Scrafty.
Apparently, Pentigan was in love with Susan the Lopunny, Jane, and Daisy.
There's also a show based off of the J-Team's adventures, but since it ended up causing a bit of trouble for the J-Team by revealing or in some cases, coming close to revealing certain things about some of the J-Team members that would make them targets. For this reason, DS is currently working on the concept for a reboot of the show, having reimagined her friends and adventures to fit into a fantasy setting.
The Smurfette Principle:At the beginning, the only girl was The Chick, Daisy. Then Janecame along. Later on, Palkia was revealed to be female, and it just snowballed from there. It's gotten to the point where there are slightly more female main characters than male ones (not counting gender-bent ones).
Socially-Awkward Hero: Most of the main cast, to varying degrees. Sakura is notable due to being this is in the past, but when she's introduced in the RP, she's actually very sociable.
After Wolf and Anom switch bodies, Jane attempts one, asking Anom-in-Wolf's Body a question Anom would know the answer to, but is disappointed when he doesn't give her the answer she was hoping for.
Before that, Pentigan attempted one of these by asking a question Wolf would know the answer to. When Anom nearly fails to answer the question correctly, Pentigan threatens to send out his Victini to attack him. He is called out on it.
Jane and Fool end up fighting a swarm of Ariados while searching for Troll Orbs.
A swarm of Ariados nearly killed Every in his backstory, leading to a lifelong fear of the species.
Spontaneous Weapon Creation: One ability of Aura in this continuity is to make Hard Light weapon constructs, similar to how Lucario use Bone Club in the Pokémon anime. Tagg, however, is incapable of creating anything but chains without using his dagger.
Stealth Hi/Bye: 'Dark' Super Nerd seems to always do this, with poor old regular Super Nerd waking up with no clue of where he's been.
Story Arc: Each story is based around arcs that are based around greater sagas, not counting the numerous individual character arcs:
J-Team Assemble Saga: The assemblage of the J-Team and its codification as a concept, consisting of the Sinnoh, PMD-1, Unova-1, Ranger, and Gold Conference Arcs.
Upheaval Saga: The AU Arc.
Aftershock Saga: Dealing with the aftermath of the AU and consisting of the OI, Hoenn, and Infinity Keystone and Kanjoh-1 arcs.
Paths Saga: The PMD-R and Kanjoh-2 arcs, taking place partially concurrently.
Cipher Saga: The J-Team's fight against Cipher, consisting of the Unova-2, Holonquest, and Orre arcs.
Recovery Saga: The J-Team dealing with the aftermath of Orre, consisting of the Kalos and Ranger-2 arcs.
That Poor Cat: Has happened a few times, with the cat in question each time being Artemis, DS' Purrloin. This continues to happen even after she evolves into Liepard. Not always played for laughs as it sometimes occurs when Artemis is hit by an attack from another Pokémon during a battle.
The Good King: Of all of the Warlords in Ransei, Sabaku is the only one that always puts the safety and livelihood of his people ahead of any kind of desire for power or conquest. He even submits himself to civilian authority, and asks for permission from the leaders of Terrera's guilds before he officially declares war on the Nixtorm-Valora Alliance.
Teala the Druddigon takes one after taking Oslwa training.
Stratus defeating a holographic Mewtwo about as powerful as the real one.
Sakura progressively gets better as the RP goes on, as do some of her mons like Dylan and Seth. Sakura takes a particularly big level in Orre once she steals Verax's gun just before he was able to shoot her dead and held him at gunpoint until his Hydreigon bailed him out. This is only minimally dampened when it's later revealed he still could have easily killed her. It culminates in her becoming a succesful ninja superhero.
During the group's stay in Crewe's home for the holidays, Myra gets a piece of mistletoe, and hangs it over Alyssa and Jeff. Eventually, other people end up under it, such as Sakura and Rawst. When Crewe and Straw ended up under it, Crewe ended up kissing Doopliss, in human form.
Similar shenanigans happened when several members attended a Christmas at Ren's family's manor in Johto.
Urban Warfare: Showcased in the battles of Celadon and Goldenrod during the AU arc.
Villainous Legacy: The Seven Jerk Dragons transformation of most of the human population of the PMD-B timeline is directly responsible for the state of that universe when the J-Team visits it. Specifically, Bahahkun's descendant Maleficent had designs on starting a whole new dragon war, which were cut short when she died.
Villainous Valor: Despite being knowingly outnumbered and outmatched Melinda's mons, and her Chandelure in particular, chose to fight against the J-Team anyway after her car got forced off the road after being chased for capturing DS and Mirage.
Virtual Soundtrack: Players often use music to set the mood of the scene they're doing for better atmosphere.
Vitriolic Best Buds: Crewe and Vierr constantly make sharp jabs at each other (the former quite literally), yet they still seem to consider each other friends.
Voices Are Mental: Played straight when Jane and Palkia, and DS and Artemis switch bodies. Averted when Wolf and Anom switch bodies.
We Are Everywhere: Tagg actually says this almost verbatim to refer to the PEFE's very long reach throughout the regions.
But a solemn morning when her parents read: "Solana Malkewitz, officially dead"
I can't help him like this, and I'm not letting my son die the same way I did!
Thanks for saving my boyfriend.
Mel is... dead.
What Happened to the Mouse?: There were a few of these, including the random disappearances and reappearances by Mewtwo, the fate of Pink the Audino's parents and what happened to the Azure Flute, but these have since been answered in later story arcs.
World Half Full: Tagg points out that while the universe of PMD-B isn't perfect, it certainly isn't a total lost cause.
World of Weirdness: The world of WAAPT is in a word, strange, but most people go about their regular lives.
Written-In Infirmity: Jane's writer getting a period actually factored into the plot, and players have had their characters catch any illness they've gotten in order to excuse any non-involvement in a plot.
Yank the Dog's Chain: The PMD-B timeline can be viewed as this at first, since the AU managed to rid itself of its biggest problems only to have dragons turn most of everyone into Pokémon and mostly rid the Earth of human civilization.
It's implied during Portales' backstory that the homeworld of the Elgyem species somehow got destroyed or otherwise rendered uninhabitable, meaning that the Elgyem and Beheeyem that managed to make it to Earth may be the Last Of Their Kind.
Fool, Michelle, and Roderich were permanently banished after the former two ended up killing the Simipour they were supposed to be forcibly mated with due to troop hierarchy.
This also happened to former Scolemis soldiers who defected from Dragonspiral Tower in the AU, including Mira.
Anom, Luke, Fool, and Mezzo all have blue hair. Wolf and Gamer have green. Sakura and Maggie have pink. Anom mentions having brown hair in the story, though. This is either artistic liscense or simply a Retcon.
Played with in Gamer's example, as he actually dyes his hair that color. As does Sakura.
Your Cheating Heart: Ammy ends up cheating on Umbra with Vlad, due to confusion regarding her feelings, resulting in an egg. They do end up back together though.