PokéFiends provides examples of the following tropes:
Adaptational Badass: The Seafoam Islands, at best portrayed as a nifty resort location in the anime, has become an eight-island archipelago with a fully self-sustaining economy, large population, and the most powerful military force in the world in terms of manpower to killpower.
A.K.A.-47: Averted with Seafoam's arsenal. Everything used by one of its members in any capacity exists in the real world. For now.
All Your Base Are Belong to Us: As one-half of the paired global events to kick off the new plot direction, the militant Team Plasma under the direction of Ghetsis has just launched a full-scale takeover attempt of the entire United States of America. And they are winning.
Batman Gambit: Arceus bringing the heroes (and occasional villain) of the Sengoku era back to life in modern times to stand against the Darkness. He's banking on the personalities of everyone involved (Masamune, Nobunaga, and Musashi like to fight stronger foes; Nagamasa fights for justice, etc.) to make sure they fight the Darkness like he wants them to.
Breather Episode: The second global event, and to an extent the April/May "Alba Ball" monthly event, is this following the explosive opener of the first paired event.
Averted after all, the event has now turned into a clusterfuck, spurred off by a wayward IED targeted on the president of Seafoam and now devolving into an actual return of the Big Bad, resulting in a sea of monsters born from the souls of the humans attending.
Continuity Reboot: Not for the site itself, but the Republic of Seafoam was brought here and reinvented somewhat from how it appeared in Stardust: The Dark Pokémon Wars. Some characters and most of the plot have been carried over, though with some notable changes, for example Team Rocket not being the major adversary on PF.
Day of the Jackboot: At the conclusion of the Castelia event, a cut to another scene shows Ghetsis and Colress strong-arming the President of the United States into doing their bidding, including authorizing an "Arbok Defense Force" that is supposedly to hunt down Team Plasma, but actually is the villainous team.
Does This Remind You of Anything?: The two events to kick start the site's plot. One involves the collapse of a symbolic building in Castelia City's skyline due to heat and stress on the building's internal section, thanks to a bomb fueled by, well, jet fuel. The second event involves the explosion of an atomic bomb in the heart of Saffron City.
Eagleland: The Republic of Seafoam is unquestionably a type 1.
Elaborate Underground Base: Per the norm, Team Rocket had one in Goldenrod City, but then a band of vigilantes came to call in search of a database. A very destructive search.
Eldritch Abomination: The Darkness, the antithesis of Arceus, is a swirling mass of darkness that appears to each person as their own perception of it. Some perceive it as worse than others.
Enemy Mine: Archer, leader of Team Rocket, most recently contacted Seafoam in an attempt to offer a truce, more or less, until such time that the greater world threats were under control.
Everyone Calls Him Barkeep: The site admin has not given an official name to the Darkness creatures that have showed up in Saffron, hoping to invoke a popular designation based on what most of the players call them. The officially-accepted designation for the weakest of the humanoid types is "Darkspawn".
The main contender so far for the new, bigger and meaner types, a fused mass of Darkspawn approximately the size of Bahamut SIN, is "Duskdrake".
Evil Evolves: At a startlingly-rapid pace too, apparently. The very second world event has given us the boss-grade 'duskdrake' type creatures that are the size and approximate toughness of old-school D&D dragons. The original Darkspawn also got up-armored in the same go.
Expy: And how. The board even allows people to "Pokemon-fy" characters from other works to suit the universe. So long as the characters are worked in in a believable manner, the board's staff is okay with almost anything.
Attack on Titan: Hanji Zoe was the first to fully appear on the board (unless you count a character whose only resemblance is using an image of a gender-swapped Eren), being placed as a fully-armored Mandalorian intended to evoke the image of the vilified Mad Scientist Demagol, even going so far as her well-known nickname amongst the Mandos being "Demag'ika" (Little Demagol). Plans are in place to make expies of Levi and Petra, but so far those three are it.
Call of Duty: Various characters typically find their way onto the board one way or another. So far the site has expies of Ghost and Joseph Allen.
Full Metal Panic!: Tessa and Leonard Testarossa, as well as the Whispered powers, were added to the board due to the board owner's love of the dojikko captain. The creator of Leonard went as far to set up Amalgam on the site as well. The character Paige Hamilton also was reworked into a Kaname Chidori replacement, while a character named Sophia was written up to serve as the first Whispered.
Project Arashi: To the great horror of everyone familiar with the character, a (vastly underpowered) version of Chao Lingshen has been imported, along with Seno and Motoko. The scenes with Chao in the new world event have directly stated that Mahora (or at least its students) exist in the world, and with the Godzilla Threshold considered to be crossed by the next evolution of Darkness creatures, the rest of the Kuro crew are being called in.
RG Veda: Nature loving Ashura Quatre wandered onto the site with a Pokemon team based on his abilities in the series.
Tales of the Abyss: Locke and Ashen Fabrel are too similar to Luke fon Fabre and Asch the Bloody to be funny.
Tiger & Bunny: Both Keith Goodman and Ivan Karelin have found their way onto the board as Keith Goodmann and Ivansen Kaverin.
Touhou: Jiang Lifen, Althea Carinthea, Lore Merritt, as well as Calathia and Chrysthane Scarlet, are all ports of the Scarlet Devils Hong Meiling, Patchouli Knowledge, Sakuya Izayoi, Remilia and Flandre Scarlet respectively. Satsuki and Haru Yūrei are ports of Yuyuko Saigyouji and Youmu Konpaku.
Genre Shift: The site RP started off as your typical Pokémon affair, a bunch of happy children getting their pet Olympus Mons and going on their little journeys. But then this group of weird people joined and set up a military nation. And now suddenly the region of Unova (and by extent the entire United States) are in a straight-up, Call of Duty-style war, Saffron has been nuked, and there are pus vaginas spewing Eldritch Abominations where there used to be the city.
Guns Are Useless: When Darkrai shows up in Saffron to help combat the Darkness creatures spawned in the aftermath of the nuclear event, he specifically tells the Seafoam soldiers that their guns might not actually work on them. This isn't actually the case. It's even less accurate after he empowers their small arms.
Promptly lampshaded by the soldier who said that Darkrai should have buffed the heavier guns on the vehicles.
Improvised Weapon: Many and often, notably Masamune using the steel pinions of a Skarmory as stand-in swords, and Nagamasa using a bench as a bludgeon until he got careened into a tent that happened to have a real steel lance in it.
Militaries Are Useless: Taken out back and executed at PF. The Republic of Seafoam is run (both by characters and behind-the-scenes by players) by military veterans across a variety of combat-related fields, none of whom tolerate this trope. In fact, Seafoam is so competent that its military is seen by some of the other, non-Seafoam players as instant resolution to any conflict their full force comes into, which is why a lot of events add extenuating circumstances to limit the numbers and firepower they can bring to bear.
Mission from God: Arceus brought back the Conquest era heroes with the intent that they would duke it out with the Darkness.
Not Me This Time: The party that had been investigating potential source points for the Armageddon prophecy at Sabrina's behest has made no secret of the fact that they believed Team Rocket would be behind it, and proceeded to get heavy-handed with several Rocket agents and one of their bases accordingly. Turns out that Team Rocket's doing nothing more nefarious than running guns.
Summon Bigger Fish: With the relative ease with which the defending forces at the battle in Indigo Plateau were putting down the humanoid Darkspawn, the Darkness upped the ante by creating multi-Darkspawn fusions that are armored, faster, stronger, and roughly the size of Bahamut SIN.
Title In: One of the players is fond of starting every first post in an event or thread he joins by putting one of these at the top. No surprise, given that he's done the same in Project Arashi and Brothers in Arms, and the ones here tend to follow the format he uses in Project Arashi. A few other players have started picking up his habit.