These are what we call the 'YMMV items.' Things that some people find in this work. We call them 'your mileage might vary' because not everyone sees these things in the same way. This starts discussions in the trope lists, a thing we don't want. Please use the discussion page if you'd like to discuss any of these items.
Big Lipped Alligator Moment: Several back when this thread was in Forum Games, mainly due to random people who don't want to participate in the arcs showing up and doing stand-alones. Highlights include:
Kyurem accidentally calling DS' Xtransceiver. (one has to wonder who it was really trying to call...) Somewhat subverted later on when this leads to the discovery that only those who have Minds of Crystal are capable of understanding Kyurem's speech.
A few of the Cipher Admins. Allen in particular is regarded as this in and out-of-universe for being smug, passing the Moral Event Horizon on morning strolls, and showing no hint of being remorseful or even remotely phased when confronted with his crimes.
Die for Our Ship: Quite a few in-universe fanfic writers had this in mind when shipping the trainers.
Hilarious in Hindsight: While inside 'M's organic core, DS has to hold Anom's hand in order to help him get through it without freaking out. One of the first things that seem to come to Anom's mind about this is "I hope Wolf doesn't misinterpret this." Later on, Anom and Wolf get heart swapped by a Manaphy at the beginning of the Oblivia arc. Not wanting to tell the others, they decide to pretend to be eachother. This leads to some interactions between Anom-pretending-to-be-Wolf and DS that cause the real Wolf to essentially become jealous of himself.
Cilan dyed Anom's hair green at one point early on in the Unova arc. And as mentioned above, Anom later ended up switching bodies with Wolf, who has green hair.
A lot of meta-conversations and in-RP conversations have subjects that become this trope later on.
Some of the events back during the Unova arc seems to predict some of the things that would later be revealed to be part of the plot in Pokémon Black 2 and White 2.
Zero remarks here about Dittos having twins. Later, Straw meets Eskay's Ditto, Doopliss, who looks exactly like Straw in human form, only with a goatee.
Les Yay: When Mira the Mienfoo first meets DS and her team, and witnesses Artemis the Liepard fight off a Beartic, Artemis has Bishie Sparkle from Mira's point of view. Artemis later sees Mira the same way after Mira evolves into Mienshao.
When DS is trying to figure out her feelings after Wolf kisses her Mira talks about how one sometimes have to deal with discovering feelings one has never felt before when they meet someone special. While Mira is talking about this, she's staring at Artemis.
There hasn't been a chance to reveal it yet, but Bonnie the Weavile has a girlfriend. A Scizor named Clyde.
Marceline the Gardevoir had a kinda Precocious Crush (It's complicated...) on Lily the Lilligant almost since she evolved into a Kirlia. This was recently reciprocated.
One of those threenote Eskay x Psyche became canon.
Skye has also become one, having various ships with several others, notably, Luke, Caliburn, and Diane. Skye X Diane has become canon
Herbert, as a new PC, had already gained three ships: Herbert x 'Sarah', Herbert x Sakura, and Herbert x Carol. Later, Crewe X Herbert also became a thing. To say nothing of his Ho Yay with Sam and Joseph...
Crewe has an incredibly good name for Portmanteau Ship Names; Crab, Craw, Crowe, Cruke, Crouch, Creddler, Mewe, Craisy, Cryche, Viewe, Crewebert, Creskay, Skewe, Criane, Crent...
Defied. Daisy tries to be this, and Gamer sometimes lapses into this, but the rest of the group keeps it under wraps well enough that they have their losses and flaws just like everyone else.
Memetic Badass: Lake, who after all is a mon on his own and has defeated Red twice. Since he's his own mon now, he can also speak in the discussion thread. And in the PEFE Chatroom, where he is the most badass (and adorable) creature imaginable, capable of using Judgment among other equally incredibly and fictonal attacks.
Mike the Techie. He's basically the WAAPT equivalent of Chuck Norris now.
Pink the Audino, who was blackmailed by 'M and turned into part glitch. Several of the other characters even stopped what they were doing just to give her a hug.
Each of the trainers have had their moments of woobieness, with special mention probably going to Anom (especially during the Oblivia and the Alternate Timeline arcs) and DS (again, especially during the Alternate Timeline arc).
Doc, Tagg's Audino, who's mother was killed in front of him and who also got turned into a Shadow Pokemon.
Tracer's Salamence, Nadia, who not only had to deal with Tracer missing her evolution but also getting temporarily grounded after Tagg's Hydreigon broke her wing.
Riku, Lyuri's Sandslash, being responsible for the death of Lyuri's parents when he was just a baby and suffering a lot of guilt because of that. And also for being constantly bullied by one of his teammates. And even then he was involved in an accident that got his best friend, Zap, hospitalized, fortunately, things seem to be getting better for him.
Edward the Dratini, his first appearance has him getting beaten up by his first trainer and the scene where he fought Goldie was heart wrenching.
Daisy didn't realize that Josie the Medicham was male. To be fair, 'Josie' is a rather feminine name.
Happens again, this time with Virizion. The Mysterious Old Man claimed that it is male, but after an extensive debate between everyone, a verdict was found and now Virizion has a set gender. She's female.
Pentigan's Pokémon form is a Lopunny.
Most of the team was confused as to whether Mezzo was a boy or girl when she first joined. During the GC Arc, she invoked this in the fanbase by making contradictory claims about her gender.
Carl (A male Panpour) tries to avert this by not evolving.