As one of the main developers for Luna Pixel Studios, the creators of modpacks such as Better MC & Medieval MC, the most common complaint I see amongst players is that certain features do not fit their playstyle.
All of our Medieval modpacks feature EnvironmentZ & Dehydration on Fabric, and Survive on Forge. A lot of people do not enjoy the thirst and temperature features that these mods add, so a possible solution to this is giving players the option to disable certain mods/features from their singleplayer experience as part of a user-friendly, customizable onboarding process.
Another common complaint is that the button to open a backpack is B, and the button to activate Narrator is CTRL + B. If you try to open your backpack while sprinting by holding CTRL, you then have to press CTRL + B twice more to disable Narrator. The fix we have implemented for this currently is the Rebind Narrator mod, but we don't want to change the bind by default for accessibility reasons.
Giving players an option when they first enter the main menu or start a new world to 'disable' certain mods fixes both of these issues. Letting players change the Narrator keybind as part of this onboarding process will let players who need it to keep it enabled, and those who don't to unbind and forget about it. Resourcepacks such as Fresh Animations and Fantasy Ores are relatively intrusive to the player experience, and not everyone will like having them enabled. Having some way of letting players choose between enabling or disabling them without directly opening the Resourcepacks menu could also be a part of the onboarding process. I understand that it's just as easy for a player to manually disable or enable it from the Resourcepacks menu, but our modpacks attract a large variety of people with varying levels of experience. I have helped several people in our Discord who do not know what a file path is.
The onboarding screen itself could be a popup while the world generates in the case of mods that do not add blocks, giving players something to do while the game loads, but I'm not sure how practical this is. I feel it would be optimal for the onboarding screen to appear as part of world creation, possibly after the user finishes the screen for enabling cheats and setting the world name. The screen would need to require user attention so it isn't overlooked, so having it as a 3rd page in the Create World screen would not be practical.
Another use I see for this is editing configs via the Onboarding menu. The Immersive Weathering mod has a feature that makes certain blocks weather over time, which not everyone likes. The image I have in my head is a heading that says "Block Weathering" with a checkbox next to it, and there's a dropdown box which allows individual cases of block weathering to be disabled, as opposed to all blocks. This feature is by no means top priority - I feel that letting players disable mods is much more important.
The biggest hurdle that I see with this is letting players join multiplayer servers after disabling or enabling a mod / config. This shouldn't be an issue if the mod is only disabled for the world, but is still loaded in the game.