For some reason I think of this more as a plot or overall experience type thing rather than specific to gameplay. So many things become influenced by gameplay aspects that it's difficult to separate from it. Symphony of the Night is a decent example of where you're kind stepping backwards on the gameplay, but it's still so well constructed and the rest of it makes up for it where you don't care that it's been done "better" and the Metroid Prime games are like that too. 2 and 3 are just easy to think of as objectively superior based on simple stuff like how the scan visor operates or in the case of 3 the combat taking a whole 'nother level. But the original still has the superior story and mystery and progression and so on.
For my pick like always I was going to say Chrono Trigger, but actually I think when I played it was better than coming to it now. So I'm thinking of something like Super Mario RPG instead. Something that sorta creates these expectations in your mind of how it will play out, but then is actually quite different.
I don't mean this in a spoiler type way as I've never thought Chrono Trigger's plot relied on its answers to the mysteries being unexpected or revelations. The part I've always felt the lovefests overlook in why it's been such a game that's stood is that the plot does not resolve any of its threads, it's an openly selfish ending (or fifteen) for a game. I think that's why I was so drawn to another game I considered, God of War 2, in that the spectacle was the experience and the resolution was similarly purely selfish rather than attempting to resolve time travel paradoxes. But then I'm a sucker for when these kinds of plots throw so many balls in the air like CT and GoW2 but then are smart enough to play the central conceit straight and ignore the balls. Mario RPG, especially now, certainly isn't original in its main construction of teaming up with Bowser to fight a bigger villain, but all the stuff along the way is what's enjoyable about it and helps it be a unique experience. Really, most of its "sequels" are like that too, even something like Super Paper Mario works for me. Although I'd imagine Mario and Luigi: Superstar Saga would be my second choice from that line before even the Paper Mario mainline.
There are lots of online games I wish I could play now with the players they once had. But time travel is havoc on pings too.