While I have few problems with the storyline being jumpy (e.g. suddenly we are at the holiday location jumping over a couple weeks), since sometimes it is okay to do that to keep grinding/slogging away, I agree with you that some paths and decisions are a mess.The NTR in this is at least believable, most of the girls aren't even happy about what they're doing. They don't do a 180 personality flip based on who they're with like some NTR games.
That said, this game is still a giant mess. Both in it's writing and coding. Things happen that shouldn't or have no logic to have happened. If you send your mom to the principal, but she rejects him, he never has his fling with the teacher either, but somehow you have a picture of him doing that like the NTR scene happens.
There are scenes that have no bearing on the NTR route that only happen on that route and all content with Yuri was locked behind Ramu forcing her to do stuff. On the Alpha route, it just looks like the Dev cut the character at a certain point.
Then there's Yuri's friend she meets after exams. On the Ramu route she gets fucked, on the Alpha route they do Karaoke and she's never seen again.
Like I said, this is just a giant mess.
It's not a coding error. The mod shows the conversations about how Yuri is still abused by Ramu off camera. The mod asks if you want to watch the NTR scenes if you aren't on that route but knowing what the scene was you can see that the conversations with Yuri still talk about the events happening.While I have few problems with the storyline being jumpy (e.g. suddenly we are at the holiday location jumping over a couple weeks), since sometimes it is okay to do that to keep grinding/slogging away, I agree with you that some paths and decisions are a mess.
As I mentioned in an earlier post, in one playthrough the MC is still a very good friend of Angela, but he helped Jim get together with her (The MC is after Juno and Yuri). But the Karaoke event is just a 100% NTR/beta cuck event, no matter the previous event choices. It would have made much more sense to make an option for the MC to join in the fun from early on, since on that route Jim and the MC are halfway ok with each other.
Another thing is as you already said Yuri. I play with the mod to have access to Yuri´s non-NTR content on the Alpha and normal guy routes. It being not available on those routes seems clearly a coding error.