one that hasn't been mentioned yet is Portal 2. OG Portal was a great game for a thousand reasons but the story is, shall we say, minimalistic. I really enjoyed going through all the old sections of the labs and hearing the story of Glados in the sequel.
I love both, but minimalism should be viewed as a strength, not a limitation, IMO. Portal 2 is more polished, entertaining, and eventful-- I don't want to disparage it, but it feels more like a lighthearted cartoon with crowd-pleasing (albeit well conceived) conventional twists and turns, for the most part (the kind of direction you tend to get from most good movies and TV shows these days, except with a bit more personality).
In terms of narrative and story presentation, I don't think it's half as inspired, perfect, bold, and unforgettable as Portal 1, personally. That game completely nails all of the beats that it needs to (and no more than it needs to), and legitimately builds a simultaneously claustrophobic, atmospheric, spine-chilling, slightly disturbing, and twistedly funny experience (something which I don't think Portal 2 really even attempts to do, as you're really just occupied with having fun the whole time). And the way that it takes a throwaway joke (luring you back with a birthday party) and obsessively builds off it until it hilariously becomes the crux of the story is a stroke of genius, IMO (I don't know that there's anything in 2 that is comparable to that high).
That said, I think it was smart for the sequel to go in completely a different direction, not wanting to have to replicate the first one, and was about as good as you could expect a sequel to be.
To me, it's kind of like the difference between Alien and Aliens (both great, but the former I think is way better, despite being way more understated, and probably "boring" for a lot of people).