Phew, that's a lot to take in there. I won't respond to each point, but there's some stuff in here that's accurate, I'm sure.
I haven't read some of the routes from start to finish in a long time, so keeping up with repeated dialog over the 200+ days can be a pain. Sometimes I play it off as the characters forgetting, but other times it's just me forgetting. I mean, I've been the only writer for over 8 years, so I'm bound to forget, hah.
You know, it's funny, cause Chester's dad didn't even have a design till long after Chester's route was done. I never really planned to introduce him (cause most of what I write isn't planned). It just kinda happened in a spot I thought worked. I also had my qualms about the epilogue for the exact reason you mentioned, buuuut at the same time, I still felt like it highlighted Chester and how their relationship has progressed. I honestly struggled with his epilogue though, so it might be something I revisit in the future.
Not everything you have gripes about is without warrant, but I think some of it's weird. Some things I might never think about since it's not pointed out. Either way, it's feedback to think about! Things can definitely be improved still~