As someone who played 1-3 for the first time ever recently on original hardware - it's SH1 by a country mile.
SH1 is just an astonishing thing that stands up amazingly today, and was so far ahead of what games were doing at that time that it's not even funny.
The sequels are all great, but they haven't really matched SH1 for sheer, stupefying, out of the gate brilliance that's consistent all the way through. It's so shockingly good, so precisely sure of what it's trying to do at nearly every second, that it feels like aliens or people from the future made it.
SH2 is very, VERY different and an excellent game, and the plot (especially for the time) was extraordinary, but I don't think the overall design is as strong or as groundbreaking as SH1, and SH2's style and plot points have been copied, digested, and emulated by so many of the games that came after it that it somehow felt less fresh than SH1 to me, in 2021.