Yeah indeed, we need to do some changes here, at the very least with some of the most commonly annoying things most users would want to choose settings.
However, scrapping some sort of automation options through the gameplay we don't want to scrap, as they can feel very rewarding for the player to reach and at the "right time". Even some QoL options (the right ones) can fit this model really well - of course some like "ignore popups"/"don't pause during popups" should be available always, but I think some current and potential new ones could fit very well under research still.
I think you put it nicely - if something can be frustrating, it should be a setting by default. If something improves on something/makes it easier/automated it should in most cases be fine (and potentially even better!) to be part of research.