The games here are
Final Fantasy VII (1997) vs Final Fantasy VIII (1999)
Parasite Eve (1998) vs Parasite Eve 2 (1999)
Resident Evil 2 (1998) vs Resident Evil 3 (1999)
(You could place Parasite Eve between FFVII and FFVIII since it came out between the two and was used to prototype some of the tech for FFVIII)
The leap in quality with the human character models is especially impressive. Look at Sephiroth's beautiful visage here and just think that Square went from that to feeling like their animation was convincing enough to carry an entire sci-fi drama movie with a realistic human cast in less than 5 years
spoiler
Then of course you had Oddworld Inhabitants who came right out the gate with movie quality CGI. Their characters all being fish-faced aliens instead of humans probably helped
Vagrant Story is one of the most remarkable games of that generation and I always find it strange to find it missing from retrospectives of that time. It was way ahead of its time in so many aspects it's insane
Yasumi Matsuno is not allowed to have a good game become popular :/
I feel like a lot of the non-Final Fantasy SquareSoft games just blurred into obscurity for most people. For the most part, I kinda get it - back in those days I didn't have access to the sheer amount of games media that exists online today.
Hell, I'd argue that too many people remember of Vagrant Story on the basis of it somehow being Ivalice.