I mean, a little bit yeah, but that's not it, it's more the fact that their behavior is inconsistent... and like, they just met, chill the fuck down.What makes the Twins' reaction stupid? That they called out the MC in a harem game?
As for redoing the entire skill tree, that might take more effort to do now than implementing it, depending how skewed his planning is from his implementation. I don't think it's unfair to compare a VN to a regular novel and, in that sense, it's very easy to have far more of a story planned out than you have written down. I can't remember the release date of Ep2, but it was a pretty quick release by single dev standards, especially since this isn't his full time job.
As for the rest, it might take more effort now, but in the long run it'll be better for the game (and the dev's health, most likely)... most people seem to be cheating anyways, so there's no real point to it as it is (and it IS a bit badly implemented too).