Wow that was a lot to read, but it was well done!
I'm not really sure if i got everything you meant, if you truly enjoyed the story from 0.2 to 0.3. I like how and where the story is going. So many things going on, so many questions. The MC is growing, so are all the girls, part of their background is now established (with still some mystery about them yet to be revealed, which is expected for a concluding arc for all of them at the end.) Now comes on how they interact with each other, relationships will keep growing, while the story slowly reveals itself. Lets say the story is on another arc, after the initial prologue/background thing, it is approaching the midpoint. I think things are going naturally, but that's my opinion/perspective.
Maybe you are overthinking too much? idk.
Have you played Carabdis other VN Once in a Life time? Maybe that's why I'm used to this type of writing, pacing and story overall. So, yes, everything is done on purpose, the plot revolves a lot more than just your simplistic, average normal porn VN relationships, as you said, and I love it! He did a great job with that previous game, the ending was great. I hope he sticks to his story no matter what this time as well. I believe it's gonna be great again, so don't worry, it's not gonna be like GoT disappointing ending.