I think I said this back when I first start playing the game but it's dark for the sake of being dark and not logically dark.
The more we learn about the people in the story's circumstances, the more the MC's past life makes less and less sense. A lot of that stuff shouldn't have happened.
Sadly this is achieved by not fully having the story written out (and examined) before proceeding. There's a lot of plot holes and logic gaps. Another thing that you talked about is the story progression, this is a linear VN trying to have elements of a route based dating sim....and it doesn't quite work well.
In classic dating sims, going down different routes changes the story dramatically. From the personalities of the heroines to the challenges faced by of the MC. This is why flags are important, using Chiaki as an example in a classic dating sim, you either help her NOW or she forever becomes unattainable in that playthrough because their lives are still happening even when the MC isn't around. A harem route based approach to a linear story VN just can't work unless you've thought out the whoooooole entire story beforehand.
Still a great, lovely game and I have fun with it. But the more it's updated, the more those glaring problems surface.