I wrote down "multiple choices/consequences/branching paths would be nice" on the 3rd poll but I couldn't include my whole rationale for the choice so here it is. The scene when Haxa becomes a hybrid I thought was due to my own actions/choices and I find that idea really intriguing (even though I later found out the overall outcome is the same, the illusion of choice).

During the boat hostage main story quest with Nessa I remember the player can try to snap her out of a trance when she's hypnotized or do nothing by exiting from the conversation but it would still lead to the same scene of her battling the player on the deck. So as a way for more content, an implementation of “bad routes” in which the player can purposely choose to fail and let characters hypnotize other characters. If the player doesn’t save them from being hypnotized, then maybe the hypnotized character re-appears as side-content or later in the main story. Now they’re an enemy and since the last time the encountered them they’ve gotten much stronger due to the influence of the character who hypnotized them, thus allowing for more optional content and give the player more of a challenge as a “consequence” for not saving them. So allowing players the option to not save a character from being hypnotized, thus allowing said now hypnotized character to become an enemy and/or treat the player differently than before.

For example a side-quest character was going to give the player an optional quest but due to being hypnotized (and from the player’s direct & indirect choices) they now offer a different side-quest (thus giving the player the idea they’re not being locked out of seeing content for “failing”) due to changes in their personality, will, likes dislikes, etc.

In-depth version of said example from above: An Officer Jenny located in the city is fighting a losing battle against some Team Galactic grunts in the area; and with the player’s help, her plan is for the both of you to find where they’re operating in the city and drive them out. She tells the player to meet her at a location and not to leave the city (the game will warn with something like “Hey, Jenny’s waiting on you, do you still wish to continue?) If you choose not to follow her instructions and come back to the city, Jenny’s acting strange and looks slightly off (her hair color is now the same color as the Galactic grunt’s hair color but it’s not brought up so players can notice it themselves). She now offers the player a different side-quest now to help her drive out some “bad people” in the area, being very selective in her wording to manipulate the player in helping her. At the end of the quest, at the end it is heavily implied (but never stated to give player’s room to interpret) that the “bad people” the player helped defeat weren’t actually bad people and you just indirectly helped Team Galactic achieve a goal of some kind (maybe steal a device that helps their goals, put the city under their control, etc). Then after the quest and coming back into the city and talk to Jenny, she’s been fully brainwashed and asks the player who is Jenny (since she’s been so brainwashed her whole identity and the way she talks/acts is changed) maybe through dialogue saying “Huh? Jenny? I don’t look anything like those cops!” since the player character doesn’t have dialogue. However, she still remembers you for helping her and gives you an item that benefits the player (example: if you encounter a Team galactic member outside of a quest, they won’t battle you, act friendly, and give you some unique dialogue). Then afterwards you can talk to her after completing the quest and show how the hypnosis/brainwashing has affected her through dialogue how she still has memories from when she was Officer Jenny but everything is warped (her chasing bad guys when she was a cop to serve the public good has her chasing after “bad guys” people with pokemon to serve the public good of Team Galatic), if you press her on more serious or personal questions she briefly gets confused, starts panicking from the brainwashing conflicting with her past memories of reality “Wait, did my family always looked like…me?” goes completely silent “…” for maybe 2-3 lines to make it awkward for the player and imply she’s realized something before the brainwashing/hypnosis kicks back in and she goes back to "normal". Thus, given a dark and satisfying conclusion to the quest's story and allowing players to question the consequences of their action (like the whole story portion with the casino).  

tl;dr implement choices, which the player can purposedly choose to fail, which allows for the hypno content/themes to appear and further lead to the game optionally difficult, and make “failing” fun. Can be implemented and scaled from mains story to side-story or completely separately as side  content.

I appreciate taking your time reading this post and considering the feedback provided from the players via the polls, Discord, and other sources. Thank you and have a good day.

Also one complaint (I don’t know where to report issues/bugs): I would appreciate that one side quest in which you're being stalked in the dark forest needs to be less frustrating (if it hasn't already been fixed); the stalker once you're finished battling her follows you way too quickly. I had to battle her about 20+ times till I found the exit. The way you’re supposed to go could be better conveyed. It took me over an hour to find the exit and see the big guy (I think it was slowpoke, I can’t remember lol). It’s the only quest I encounter that I disliked.