I think, overall, any of those situations where you have the "y/n?" queries (eg: diving into water with no swim-skill, leaving a town, quitting, saving+quitting), those should be a pop-up window -- like the tutorial windows -- with "yes" and "no" buttons on them, so they can be clicked.
I started playing the Steam version just recently (had played the ASCII version for many years), and tried as much as possible to play it with the new interface elements available to me -- almost entirely using the mouse. The one thing that was occasionally brining me to a halt, and breaking my immersion in the game, was those yes/no moments, because they weren't accessible with the mouse at all.