You really hit the nail on the head with most of your post, but this is hands-down one of my biggest "problems" with the game (with quotes because it's still easily one of my favorite H-games ever, despite my disappointments). There are so many little touches and ~flawless~ build-up of suspense to certain moments that just... never actually pay off, or result in some really lackluster conclusion.
Like EVERYTHING with the two thugs. My first time playing through the game, I absolutely loved how simultaneously threatening and incompetent they were, and wish the game would've given them more time to actually shine. It really added some unique appeal to the idea of them capturing anyone, especially the teacher, Sui. I think I honestly held my breath throughout the entirety of that scene where she surrenders willingly to them in order to spare the other two girls, because it was so clearly building up to that moment, and everything with her failed escape to being immediately recaptured just heightened that sense of dread and anticipation.
Even the ghost that ruined her escape adds something, where you can see it stalking Sui when she walks off-screen earlier on and it blocks your path, forcing you to find another way around to catch up with her. I absolutely adore that kind of vaguely sinister tension growing over time, since so many games seem to lack that sense of intention with how they are written.
And I won't lie, I did still like that scene with Sui and the thugs when it eventually happened. I liked it quite a bit, actually. But I still feel like it didn't land as well as it should have, since Rixa is also there for pretty much no reason with nothing to actually contribute to the scene beyond drawing focus away from Sui's big moment. It either should've just been Sui there, or she should've had an earlier one as well with both of the thugs. Or hell, even just the faintest implication that it was happening while she was off-screen for so long.
Another one that really bugged me was all of the foreshadowing between the thugs and Norea. There's a genuinely intriguing thread of Sui attempting to drive a wedge between Norea and her two lackeys by consistently pointing out how she's losing control over them... and then Vena just kills them before it can result in anything. Sure, they do come back as ghosts and get hilariously distracted from attacking Vena by finally getting the chance to "party" with their boss, but I don't think it was worth the trade-off of them having no further dialog or personality by that point to drive it home. The whole tension of the "they were already planning to betray her" side-story amounts to nothing, because when the scene finally happens, they are really no different from any of the other random ghosts. The only positive thing about it was the initial reveal, where the game makes you go back and find her like that, like the punchline of the joke where the set-up was them mysteriously bolting off-screen earlier without any explanation why at the time.
As for the ending, I had the exact same complaint about Vosmug's last game, Xenotake. GHV has it much, much worse because of how seriously it suddenly tries to take it with... whatever the hell happens with Vena and her heart, I'm honestly not 100% sure what it was trying to get across there with how much exposition it tried to spit out in the last ten minutes, but the tonal shift felt
super jarring. But there really should've been some way to ultimately fail and get a bad ending with everyone trapped in the house, or at the absolute least, give that fate to Norea as the game's main antagonist. The true villain of the game has some hints of characterization if you squint hard enough between the notes and the wasted flashback sequence, but has no real presence in the story as its told, so defeating her doesn't feel like enough of an accomplishment to justify the weirdly saccharine epilogue that just drags itself out foreverrrrrrrr.
I swear, this game and Tails of Azeroth are the banes of my existence, because I could rant about them endlessly for VERY different reasons...
(for the record, I'm also sorry for the essay, but begging on his blog for bonus/alternate scenes to be added or a spinoff "sequel" starring Sui has gotten a bit old, and the next game looks like it won't scratch the same itch... so I needed to vent about the story somewhere!
)