VNs are not art, I´m afraid. You are talking about art. You can´t compare VNs (or videogames in general) with artistic films or literature. Videogames, so far, are entertainment. Maybe in the future will be made the "Citizen Kane" of videogames, and videogames will be considered art. But it´s not the case so far. And the definition of "entertainment" is escapism of reality.
Anyway, it´s laughable to think that this VN (or any other VN) can be "instructive", used to "show criticism of real life", "suggest potential for future", etc. I don´t think even the dev has ever thought about his game in those terms.
And yes, a villain of a game can be an unpleasant character (although the best villain has some kind of attractive and generate both repulsion and attraction. Think about Dracula, for example), but, if the players can´t stand the MC of a VN and/or the Lis... the VN is a disaster. It´s not that players can´t stand the characters of this game (I think), but truth is that there are 26 pages of comments here, and I would say that about half of that are people that complain about the characters. And think that most of the people doesn´t bother in even leave a comment if they give a try to a VN and doesn´t like it. They just delete de game from their HDs and forget about it. Maybe that´s the reason there is ONLY 26 pages of comments after 5 updates of this game.