Let's see...I usually cut things for the sake of time, but here's a couple of design decisions
MewYou:
-Field moves like Rock Smash were cut out because it goes too hard against player's expectations that they'd be able to smash them. Just being able to levitate over water throws most people off and they assume it's a bug at first.
-A level at the end where you navigate through Mewtwo's New Island Dungeon. The ending of the game is suppossed to resemble the first movie, but I really didn't want to make tiles for that or have to involve a bunch of canon characters in cutscenes.
+Added content: I saw that most players never even thought about the visual markers I'd put on every map, so I ended up adding an NPC who clearly states what they are. The same goes for talking to NPCs who were on top of ledges; for some reason a lot of players tried doing that, so I added it in along with talking to NPCs behind fences.
Bonfire Stories:
-Having each character offer multiple stories at once instead of unlocking them one at a time
(unlocking doesn't actually happen yet either, there's not that many stories implemented). If a player was trying to keep track of all their options that'd be like,12-15 at once. Yeesh
-A story that takes place in space, because it made me really want to make a Eeveelution that evolves in zero gravity but this isn't a fakemon game.
-A crossover story taking place in
Ethereal Gates' Leneka region. Didn't even end up running that idea by Evan because again, decided on no Fakemon.
-In 'Duplicates' there were originally battles against household objects in order to clean them, and the items would've used only HP restoring moves (Old Vase used Gather Dust!) or moves that didn't do anything. I kept Minccino's moveset but did pokemon instead because they're way more interesting, even if it's kinda wacky.
-A time based event in 'The Changeling' if the player tried going into town after being told not to. It would involve being chased, but would've cut the player off of the second part of the forest and I didn't want to have branching paths.
-'Flashing Lights' was way longer and more hostile. The story still revolves around "the main character has memory loss and so is locked in a time loop while the situation slowly gets worse with each loop" but that was toned down a lot so that the player doesn't have to come to that exact conclusion to follow the story
(just know that freaky things are happening).
-A story called 'The Huntress' was re-written to 'Ice Princess' because the twist at the end was that the protagonist was a murderer and that's why so much bad stuff had been happening. There's already a story in the game though where the player gets to be a bad guy and there's karma-tic justice, and that character is more interesting and fun to play as.
+Added content: Keeping the TMs after each story. Originally that wasn't suppossed to happen, but players liked it and the TMs became more valuable as collectibles.