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>How different is the visual novel from the anime?
It's not different at all. They kept the plot and theme the exact same. It was a pretty good adaption, the original Ran->Sem episodes, not Cross Mix. Obviously they couldn't adapt everything from the VN because the VN has literally hours upon hours of material.
> I guess a lot of sex scenes must have been cut out.
Yes because the VN has 4 different endings and each ending path has its own unique sex scenes.
> There was even some woman who I guess was Riko's friend who also joined the cult.
Yes. Her name was Naomi. They cut her out of the anime and instead gave her screen time to Sakaki. Naomi was as a undercover agent working directly for Majima. When Riko was trying to get into the cult she couldn't figure out how until Naomi approached her and told her how to get in. Naomi was pretending to infiltrate the Cult, just like Riko, to save her fiancee; when in reality she was sent by Majima to trick Riko into joining the cult. Also Naomi needed to capture Riko so she could be promoted to Majima's right hand-man. I guess the instructors in the cult gain status and rank up by getting beautiful women into the cult, the more beautiful the woman the better. So Naomi capturing a top tier woman like Riko basically guaranteed her spot as the #2 most powerful person in the cult behind Majima.. also she's basically obsessed with Majima and will do anything to please him - so she goes aggressively after Riko.