Things I've cut:
1. Evil Storyline. While it was intriguing all on its own, it wasn't compelling from a video game standpoint. The vast majority of gamers choose paths of "good" when possible. There are exceptions, but those are sort of rare in the industry. Instead, I chose to combine both versions of my storyline into something a little more compelling. Namely, that the player is going to be trying to do good the entire game, but more often than not, bad things happen as a result of those good deeds. It is more interesting that the player chooses "the lesser of two evils" at each choice instead of "is this the good guy option, or the badguy option?".
2. My original "Sin" System. It involved equipping an item that drastically reduced stats of the character and ran down a timer so long as it was equipped. Once the timer ran out, the item was unequipped, changed to a powerful item, and then equipped back on the character. It was boring, easily exploitable, and didn't really provide any interesting player choices. Instead, the item now only influences/changes dialogue when equipped (it still hurts your stats) and I opted to provide conversations in "safe spaces" so you can grind these out... but the bigger bonuses come from dialogue just before battle (so you have to take the penalty in combat in order to get some of the largest gains towards transforming these items).
3. A Trading Card Game. I spent a significant amount of time designing and coding one. However, the older I got... the more I decided the Card Game could stand on its own if I ever decided to really do anything with it. I also decided mini-games were a waste of time since I first created it, as they distract from dev time and aren't really "interesting" to a player beyond the first 3 hours they play them. Essentially, they're a feature that "gathers dust" unless you make them necessary somehow. The novelty wears off fast.
4. Pacifist Mode. I had my game originally designed so that you could be a 100% pacifist if you wanted to be. I removed it entirely as it made it difficult for me to keep trying to come up with methods that you could solve some problems by not engaging in combat. I eventually decided on a "Diplomacy" type system where it could be used on reasonable sentient creatures. Though, what you might sacrifice in order to "not engage in a fight" fit in with the player choices from option 1. What kind of deal would the player make if they decided to not wipe out the bandits and work out a compromise with them instead? More interesting than just not engaging in combat. Plus... wild animals can't be reasoned with. They just want you dead.
5. Achievements. I love achievements in video games. I love collecting them all. However... They're not really good for my game. They would enforce specific methods of play. They would enforce "save scumming" quite a lot to get multiple options. Creating multiple save files for a single run. Using guides to get all of the achievements possible. I just ditched it. The point of the game is the story and the player experience. It isn't about collecting things and "seeing all the content". It's about one player being able to talk to another player and sharing their unique experience with the game, because they chose different paths and did different content.
Those are some of the things I've cut. At least, off the top of my head. I know I've cut a crafting system as well, but that was early game, before I ever had a storyline. I cut it 'cause it was tedious and didn't fit with the gameplay I wanted at all.
