I haven't played the VN but I hear it was adapted quite well. So I assume it was a source material issue. But I also hear it only covered the first part of the VN and not the whole thing and apparently it gets significantly better from there.
The whole anime was shit besides the ending & piano girl's story (Setsuna and male MC were some of the worst characters I've had to endure). But like I said, the ending was actually really great so I feel like it ended appropriately despite not being fully adapted.