Touhou Ningyougeki

A long time ago, Patchouli Knowledge grew tired of Marisa Kirisame coming and stealing her books. Therefore, she made some puppets with decent intelligence and power to keep the library safe because she doesn't believe in Hong Meiling at all. Unfortunately, one of the manuals had been stolen by Marisa and the thief herself made a lot of puppets for pilfering. When they came, Patchouli impatiently blew both armies of puppets and a part of the library away, included the remaining manuals. After the incident, puppets have been reproducing in the wild, and people got used to them. Time passes and they are now served like pets to everyone.

Touhou Ningyougeki (東方人形劇, lit. Touhou Puppet Play, also commonly referred to as Touhoumon) is a modification of Pokemon FireRed (some say a Pokemon Emerald version also exists), replacing most of the 386 Pokemon with as many Touhou Project characters as possible. Several English variants have been released with the same premise, but differ in various ways from the original in terms of locations, levels, obtainable Touhoumon, and other details. The patches usually regarded as 'official' Japanese patches are versions 1.53 (which keeps the typing from the original Pokemon game intact) and 1.812 (which redone the typing altogether).

Tropes in Touhoumon:

 * Canon Immigrant: There are some mons that are actually not part of the canon proper but are imported from well-known doujinshi. The most prominent example is the Advent series of mons, which originated from a famous series of doujinshi.
 * Taken Up to Eleven when one version incorporates Merry Nightmare into the mix.
 * Com Mons: You'll get bored fighting Chens, Momiji, the Aki sisters (in the grass), Komachis (on the water), Hinas (fishing, especially with lower-tier rods), and Rumias (in caves) pretty quickly. Especially glaring in early mods where the spawn ratio hasn't been tweaked (granted, you encounter Zubats everywhere, and Rumia is a Zubat equivalent).
 * Dude Looks Like a Lady: Earlier mods didn't adjust gender ratios, resulting in lots of male Touhous with very female appearance. This still happens in newer mods, but at least male Touhous are much rarer now.
 * Demonic Spider: In the early mods, Rumia. Why? It infests almost every halfway-dark places in Kanto, it confuses, it lifedrains, and it has Shadow Tag (you can't switch your Touhoumon out) as common ability. And it gives meager experience.
 * Fun Size: CYamame and Yamame are very small compared to the trainer. Other Touhoumons are generally about a third (for Chibi forms) or equal (for standard and EX forms) size to your trainer.
 * Game Mod: A good one, too. It even manages tqo balance the game even further by introducing some tweaks to the damage.
 * Harder Than Hard: Due to typing changes and overall tinkering, Gym Leader Battles can be harder than its original counterpart.
 * And it goes up to full-blown Nintendo Hard with Lunatic Mode mods. Ordinary trainers bringing multiple Full Restores and fighting with EX-level 'mons? Eeeeyup.
 * Olympus Mons: The Legendary Birds are replaced with three PC-98 characters (Kikuri, Yuugen Magan, and Konngara), while Mewtwo is replaced with Sariel. Also a kind of lampshaded since you can catch and train Suwako and Kanako, which are gods in Touhou canon.
 * One Winged Angel: Advent Yuyuko, if available, only has one butterfly wing visible. It is also faster than other Yuyuko evolutions, with high attack stats.
 * Palette Swap: The whole series arguably started off as something like this. It has since pushed into its own directions especially since the 1.8 version, where the typing are redone from scratch.
 * Some mons still feel like this due to their Com Mons status, mainly Rumia (to Zubat), Hina (to Magikarp), Mystia (to Pidgey), Chen (ironically enough, to Rattatta), and Komachi (to Tentacool).
 * Shout Out:
 * The Advent line of Touhoumons are derived from the doujinshi Advent Cirno which makes it a shoutout by extension. However, Advent Yuyuko (who has yet to make any appearance in the doujinshi series proper) is definitely a shout-out to Sephiroth.
 * The background story of Touhoumon is very similar to another Touhou fangame, Patch Con.