Can't cite my writing experience without doxxing myself, so. I'll just say I'm aware of the pitfall you're describing, and I'll be trying like hell to give every path equal attention.Personally the only game in which so far I liked the mind control theme would be Total seduction by mike Velesk, albeit it was a bit too fast, but overall as a game it was quite solid.
About the superhero game VN that you wanna make... my main issue with Visual novels is that most people literally don't know how to write and create horrible developments, even more they tend to be farming in a different way.
A typical visual novel I can find can be said to be "choose the right option to earn points/improve relationship" while choosing the bad one is just bad, while a true story is much more complex, with flags about relationships that will be remembered in the future and that people will take into account what you said.
An example of what I mean:
An amazon appears and says "all males should be slaves!", options:
-Yeah! (+1 relationship)
-Never! (-1 relationship)
A bad visual novel only cares that you get the +1 relationship, even if it isn't consistent with your future actions, while a good visual novel would reward you for actually building a consistent character and the penalty may end up being a reward in the future.
And again. Mind control is only planned as something to be used sparingly. Two characters can do it, and neither of them is the player. I've rarely seen it done well, so. Its inclusion serves as a sort of answer to that.