The Emerald League, taking place on a tropical island, where the main character encounters a Scizor guarding mystic ruins, and a Water/Steel Gyarados evolution. Author: Captain... something.

Fic focusing on the trainer appearing in Pokémon The Movie 3, with the Aipom and PokéGear. AFAIK, still ongoing on The Pokémasters forums. Author: Gavin Lupin

PokéMorphs - exactly what it says on the tin. Pokémon/Animorphs, with a family of Mews teaching Transform to a bunch of human kids, so they can fight Team Rocket and their brain worms, the Weederpies (twisted Weedle/Caterpie cross)

PokéTrek - Veridian III becomes the Pokémon World after the Enterprise had crashlanded there. Something about the ship’s database leaking info about the 1990s.

Pokémology - A human gets turned into a Ditto in a lab accident, he and his new trainer take on Team Rocket. Author: Poryhedron

Mewtopolis(?) - A city built by and inhabited by Mewtwo clones, both pure and hybrid. Some of these are put in eternal stasis for being too volatile and powerful, including a Siamese twin Mewtwo and hybrid Legendaries. Author: Vaporeon of the Mist