Spoiler
~Alternate evolutions! Expanding on AE's idea of the transcended puppets, every single puppet has one "Alt" form, which play very differently compared to their normal forms. They can be accessed by using a mystery shard on a puppet's middle evolution stage. Almost every puppet has an Alt form, and most of the exceptions don't even have Ex forms. Even minor characters like shizuha and meira get Alts! There are five mystery shards during the main game, and more can be bought during the postgame. Some puppets also have other forms, such as advent and PC98 forms.
~Your starters this time around are mostly 1.5 starters, with Reimu and Marisa reprising their roles; but Sakuya has been replaced with Kokoro in order to form a Faith/Reason/Heart triangle. Thankfully, unlike vanilla 1.5, the game dosen't drastically favor one starter over the other, so feel free to pick whichever starter you want.
~The scripts have been edited heavily, so NPC's only mention pokemon when it's contextually appropriate. Otherwise they'll refer to puppets and touhou-ish things. Additionally, some very important scripts like move descriptions, pokedex entries, and even the type chart have been edited to be fully accurate. There have also been mass decapitalizations, so NPC's no longer shout their important lines at you.
~The type chart has been edited from the 1.8 chart to bring three new types to the table! The first is wind, which is now separated from both electric and flying. The second is fairy, brought over from Kalos and modified to fit Touhou's fairies a bit better. the final type is dragon, carried over from 1.5 and is just as rare as it was back then.
~New gym leaders! While their personalities are nothing exciting, They provide for a fresh Kanto experience as you have to deal with whole new gym types. Giovanni is still around doing his earthly thing, however, and there are reports that Sabrina is still somewhere in the region.
~New puppets! Many puppets have been added into the game compared to 1.5 vanilla, such as every puppet added from UFO to DDC, as well as a few other puppets such as Rinnosuke and the Watasuki sisters. All of these puppets, along with the PC98 puppets, are available in the maingame.
~Tasteful difficulty! Like touhoumon purple version, gym leaders and important trainers in this game focus more on playing puppets to their strengths, as opposed to overwhelming you with bloated BST's or throwing out puppets that don't share the gym type at you. While this hack isn't as hard as purple, it's about on-par with some of the harder pokemon games. Well, the post-game kinda goes a bit nuts with the difficulty, but it should be nothing that you can't handle by that point. A hard mode patch is also included if you feel like the main patch just isn't challenging enough.
~Reusable TMs! Just like the later pokemon gens, TMs can now be used as much as you like. Feel free to add a bit of diversity into your movesets without having to worry about losing a TM forever!
~Help is in the zip! Various files have been included to make your life easier as a player. These files contain things like wild locations, trainer levels and type specialties, and even a list of the fully evolved puppets in the game and their stats!