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I think when people say it's the best they're talking about how earnestly it tries to live up to its concept vs. how iterative future games are.
A very, VERY large part of it is nostalgia, of course, but there's a legitimate charm to how focused on creating a very specific feel it is and how the personality of the obviously small team shines through.
It's kind of like the first Zelda; it's definitely mechanically archaic and full of bugs, but the creators had a very grand vision of recreating childhood feelings that they did as good a job as they could with the extremely limited technology they had available to them. Every Pokemon and Zelda game since has been mostly just iterating and streamlining the experience presented in that first game, instead of going back to the underlying intent of the original and reinterpreting it with the much better technology available today. This is why Breath of the Wild was such a success, it ignored most of the traditions that the series has built up and instead made another attempt to make the dream behind Zelda 1 a reality.
Objectively the newer games are more mechanically sound, less buggy and more complex, but they have yet to get any closer to what they wished to create with Red and Green, just polishing what they started, making the same experience smoother. Things like "charm" and "earnestness" are obviously very subjective, nebulous, but they're why a large contingent will always enjoy those first games more than any that came after.
