Creative Differences: Players have left in the past due to disagreements regarding how the RP should be handled.
Creator Breakdown: Unfortunately, Real Life tends to rear its ugly head and some participants either drop out to set their lives in order or take a noticeable shift in tone with their posts. Can unfortunately cause a cascade effect when someone's departure is especially messy.
Defictionalization: Pokémon in the RP sometimes go on to become part of a player's team within a RL Pokémon game, though a lot of the time this is inverted as well with Pokémon being based on ones from an in-game team. A notable inversion being the GreNinja Squad which started as an in-game team, but a combination of the player liking the concept and the team proving itself to be popular/infamous enough to cement their inclusion in the RP.
Development Hell: The ending of the PMD-R arc is currently in limbo.
Flip-Flop of God: Has happened in the past as people have changed aspects of their characters.
God Never Said That: There have been many instances of claims being made regarding statements about the WAAPTverse that have turned out to have never been said.
Loads and Loads of Writers: The RP can have up to 20+ active writers at a time, and it would be even larger if you counted the RPers who've left.
Milestone Celebration: The Re: Glitch arc was meant to be a celebration of WAAPT's 5th anniversary, though its length made it a celebration of the 6th as well.
Officially Shortened Title: We Are All Pokémon Trainers is commonly referred to as WAAPT by the playerbase.
Old Shame: The early RP isn't exactly looked at well by most of the original writer base that's still around, due to it being much lower in overall quality since it was originally a Forum Game with no continuity.
Real-Life Relative: Gamer and Meddler's players are RL siblings, as are Joseph and Emma Hudson's.
Romance on the Set: There have been couples amongst the playerbase, but most have not lasted.
Serendipity Writes the Plot: Glitchstuck Wars was made as a result of its author getting stuck in a facility for about two weeks.
Throw It In!: Some elements of the RP were created simply because someone did something random and the rest decided it was good enough to throw in. Examples include:
Jane's inexplicable Southern accent at the beginning of the RP being explained as a Hoennese (In particular Mossdeep) accent.
Champloo, Dune's Lucario, decided to make a batch of super-chocolaty brownies. It was suggested in the chatroom that, do to the sheer endorphin-releasing goodness of that much chocolate, they should be able to reduce a Shadow Pokemon's shadow gauge. This is eventually how Vega the Drilbur was purified.
Crewe being a Sneasel turned human happened when her player made a joke in the chat regarding a Running Gag... and everyone realized the idea fit in perfectly with her (up to that point improvised) backstory.
The winner of the Gold Conference was not planned, so any of the contestants could've gotten the shiny Victini at the end.
Originally, the AU was supposed to be Ret-Gone at the end of the AU arc, but due to the Unfortunate Implications of the protagonists destroying another universe for their own gain ultimately making them no different than Cyrus, the decision was made to have them split.
Robin's Pokeform was originally Dratini, before his player having a talk with Tracer's player convinced him that Robin's direct connection to Grima made the Deino Line far more fitting.
The Flickering Thing's writer wanted Jane, Luke, and Gamer's authors to be involved in the final battle of Re: Glitch due to its numerous Call Backs, but was unable to contact the latter two, while the former was too busy.
Word of God: Many statements of canon are often made either in the discussion thread, the wiki, or within the chatroom.
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.
Random Trivia
WAAPT has consistently been within the five largest TVT RPs since its inception.
Unfortunate Implications of the protagonists destroying another universe for their own gain ultimately making them no different than Cyrus, the decision was made to have them split.