I love all these. I'd add Blightsight by Peter Watts to the list. It has the creepy, psychological bent of Annihilation combined with the hard science elements common to qntm's, Neal Stephenson's and Greg Egan's books.
Would love to find more books like Blindsight, something about the way it described agency without consciousness was both creepy and extremely memorable.
Blindsight was great. I had such high hopes for their follow up novel Echopraxia, but sadly it felt rushed and under-edited, but the ideas were spectacular.
I wanted to like this, as the premise was fascinating and the word-smithing was pretty good. But something about it left me feeling a little disappointed at the end. More so the end of the entire trilogy, than Annihilation by itself though, IIRC.
I'll second your feeling on Annihilation trilogy. To me, the whole message boiled down to "my life kinda sucked, and now it sucks even more". The phenomenon ostensibly at the center of everything seems to take back seat to protagonists being bummed about it existing / their lives in general.
His book is great, but to be clear I feel like he writes exactly one book. I've read it in many forms and it's an amazing book. But don't be surprised when you realize that every book is just him trying to find a new way to look at the same object over and over again.
Very enjoyable but his short stories are great because they force him to focus on one idea instead of how his whole world view fits together.
Diaspora by Greg Egan
Anathem by Neal Stephenson (this one is a bit like doing homework but worth it imo)
If you vibe with short stories Exhalation by Ted Chiang Crystal Nights by Greg Egan isn't bad either