Eh... lots and not enough at the same time.
Morality System
I removed this after early playtesting with one. I had initially envisioned a game where "You get a satisfying story and conclusion when you play as a badguy too!". It doesn't work. Almost everyone invariably plays "the good guy" in every RPG if they can. Only the "curious" really ever play as evil... or the people who are playing the game as a game and not to get immersed. So, I axed this system entirely.
Sins
To be fair, I didn't so much "remove" this as "rework". The system in its original iteration was that players were given an option to equip very harmful items and in exchange would get new options and new dialogue in the game for doing so. The system ended up being very cumbersome for players (almost everyone would savescum before talking to each character, equip the item, talk, then unequip the item, meaning it was little more than an annoyance) and so it was removed. I did eventually rework it into something a little better. The items do still exist in the game, but aren't anywhere near as harmful to the player. The player now also gets "points" from completing tasks with these items equipped as well as having them on for conversation choices. They no longer change dialogue, but instead give you special "choices" in some conversations. There are rewards for the players picking these options and having them equipped and they're only meant to amass a specific number of points before the item itself changes into something more beneficial. Basically, there are more incentives for keeping them equipped as long as possible (you are given points towards these for most boss fights you have them equipped) and a better story reason to want them equipped (each character has one, and they must overcome it to become a better person). Oh, they're also 100% optional too. No need to equip them if you never want to.
Minigames
I had a couple minigames early on that I ditched just because I realized that minigames in an RPG just aren't fun. I had one where players would fight in a colosseum type thing and face bosses they'd defeated before, except with beefier stats. It didn't really add anything to the game, so it was axed.
The other minigame I axed was a "codebreaker" one wherein players were given the most basic cipher of the thing and expected to solve two dozen or more puzzles in the early game in order to get "unique" rewards. I may end up implementing it again later down the line (I love the concept of it quite a lot, sue me), but it was scrapped and reworked into "Find Diamonds to get Relics".
If you're curious what that Cipher hint looked like:
EJOTY. IS? GREAT! = 152102152202254319219531721815112206
Basically, it boiled down to a small group of people willing to put in the effort to figure it out and everyone else being super annoyed and not wanting to do it. So, it was axed.
It was a code that me and a couple friends came up with in high school so if we passed notes and they were "intercepted", nobody could translate them.

All they would get is an excessively long string of numbers that they'd have to find a pattern in to even begin to translate. We called it "EJOTY" as that was also the "key" for quick translation in your head (E-Jot-E).
So, yeah, have fun if you want to try to figure it out. Otherwise... yeah, it's overwhelming to look at in a game.
Dedicated Healer
I actually axed this for two reasons.
1. I wanted my players to spend their Currency rather than hoard it. Through testing and number crunching, I found that MP healing was often a minimum of 6x more efficient than healing with Potions, even if you halved the HP healed per cast and tripled the cost of the MP Potions. Players would buy the MP Potions, but never HP Potions as a result. I wanted players to spend that cash!
2. The game was far too easy for my liking with a Dedicated Healer. That is, players didn't need to prepare, they didn't need to be mindful of actions in combat, and could frequently "tune out" and watch Netflix or something while they played.
Removing the Dedicated Healer required I completely overhaul my entire game. I had to remove the traditional "get stats each time you level up" mechanic to keep players from over-leveling and removing difficulty. I had to put stats back into the game in a different way. I had to remove a great many treasure chests that gave out consumables and remove a lot of monster drops that did the same thing. I had to rework combat to rely less on stats and more on strategy and skill (or gimmicks!). I also had to invent a new system to reward players for leveling up, since I didn't want to remove the mechanic entirely.
Tutorials
Initially, I had something like 2 dozen tutorials that essentially destroyed immersion in the game and required the player learn things through text rather than through experience. I've never really enjoyed trying to teach through text as everyone tends to "zone out" when you get technical. Likewise, text doesn't really convey "nuance" that well. Making the player engage in gameplay to learn has always worked best in my opinion. I also axed a set of "in game reference materials" that would talk more in-depth about the gameplay mechanics.
I replaced these tutorials with better signposting, ultimately. Talk to someone, they give you a hint on how something works, and it's up to you to put it into practice. (For example: Thunder stun all dinosaur. You know?)
So, now the game is basically giving you the tutorial by hitting you with "trial by fire". Talk to everyone, explore, learn from your enemies, etcetera. The game only "ramps up" once it's clear you've mastered the mechanic. Namely, you've cleared the dungeon or quest that centers on the mechanic, which can really only be done if you understand how it works. Feels more organic and less intrusive now.
Steal Mechanic
Yeah, I removed this. Most because it mucks with the reason I removed Dedicated Healers. I also removed it just because I was spending too much time copying and pasting it into every single troop configuration.
Obvious Choices
I like having choices in games, but for the same reason I removed the Morality System, I removed these. If a choice should be "obvious", you can basically guarantee that it isn't. Or rather... it's difficult to stay on the "straight and narrow" in the game. Good things don't happen just because you make good choices. Most often, it's a pick between which terrible choices you can live with. I find this is much more interesting in terms of gameplay.
Granted, there are still your "goody two-shoes" choices. Defeat a bunch of bandits and whatnot, and it's good. But, it still has some negative consequences down the line. Or rather... to see the fruits of your labor for being "a good guy", you need to suffer quite a lot for it before it ever pays off. I found these choices to be far more interesting and these consequences to be much more interesting. I mean, if you wipe out all the bandits in this area, then maybe another branch of them a little further in the game has infiltrated and killed all the citizens of another town... and they rob you blind for what you've done to them (and maybe leave you beat up and left for dead somewhere dangerous, too...).
The point was merely to see what players would decide they could live with and if they would continue "doing the right thing" if it directly hurt them and their friends by doing so.
So, yeah, there's no, "save the puppy? Burn the puppy?" choices here. And, if there are... you probably aren't going to know in which way you'll suffer for saving the puppy.
Class System
I initially had the player build a party when the game loaded in like you would in the original Final Fantasy. Unfortunately, as I decided the game should be more "narrative" based, it resulted in my characters not really having personalities at all. So, I ditched this fairly early on.
Initial Dungeons
I scrapped 3 separate maps for early dungeons as things within the game changed. One of the dungeons was turned into a Tutorial Dungeon... Two more were reworked as I introduced "Collectibles" into the game so as to accommodate those features. Another dungeon was completely removed because it no longer held a purpose within the narrative and I couldn't think of any compelling reason to keep it.
Dozens of Skills
Yeah... I've lost track of how many of these I've removed. Most of them were removed when I decided, "Menu Fatigue is a thing currently happening in my playtests". I cut most of my lists down to six to nine separate skills to reduce scrolling in menus. I also created "0 MP Skills" for specific classes so that they'd always be useful even if they couldn't directly use their skillsets.
World Map
Yeah, I used to have an active world map the player interacted with. It's been relegated to "Cutscene Content Only" now. Victim of my storytelling, basically. When I finally decided on the story I wanted to tell, the world map didn't fit that story... so it was removed.
Opening
I'm not happy with removing this one. Everyone on the forums says, "I don't want to deal with a 10 minute cutscene", but I've always been of the opinion that, "If your cutscene introduces the premise of the world to me, I don't care if it's 20 minutes long". Still, I cut out all the parts of my intro that weren't "relevant" to the immediate storyline. The initial cutscene introduced every single character in the game that you would have in your party as well as a piece of information that would explain the state of the world to the player. But, it often ran about 15-18 minutes long depending on how fast a person could read.
None of my playtesters complained... But... I guess I'll try the shortened version to see how that goes over. I can always put the rest of the cutscenes in later if I need them. Or, add them back in if I need them again.