I've noticed newer saves don't present the option to skip the intro, but older ones do. It doesn't appear like the flag that controls that is being set anymore.
Muskyshep is right. That's why I asked, I haven't returned to the game for a long time and at first I thought that I confused the presence of this option with another game, but it seems to be some kind of bug since this option does not appear even after finishing all the routes.
