Huh.
I had a very different experience, obviously.
First, “strange impossible unknowable things outside of our control” very much matches the Gothic Horror genre, but second, I had some of my assumptions confirmed, and others challenged.
As for the memes, you’re right, but I think “there goes gravity” from the end of book one prepared us for that.
John’s over ten thousand years old, and that is a long time, but he’s spent that whole time with a group of people also from that era. They’ve been rehashing the same dumb conversations that whole time. I got a kick out of “none houses, left grief” because I recognized it, but also the point there was to humanize the guy. He’s a god, sure, but he’s also a dork.

The eyes revelation was huge, and continues to pay off in Nona.
Gideon the First casually put the glasses on to deliberately obscure the fact that Gideon wasn’t in that body any more, and that something was in fact horribly wrong with the Lyctor process, and that all of the efforts of book one were (on top of being strange, impossible, unknowable) futile, which again plays into the genre.

Gideon having John’s eyes unlocks the mystery of her birth, why she was where she was, where she’s from, what she was sent to do, what went wrong.

As for the “the protagonist doesn’t even matter” point, I’m sure you’ve seen that applied to Raiders of the Lost Ark.

Hopefully I’ve managed to share my different readings on your points without seeming like I’m just trying to knock each one down.