Super Mario RPG is the archetype of JRPGs of this era and illustrates what is missing from current games. It doesn't need a super complicated ability or equipment system or ultra-fast battles to keep players entertained. It is such a perfect blend of platforming and RPG elements that has since not been matched anywhere (though the Mario & Luigi games are fun). Battles are simple yet still require precise timing to excel. The story is fun and whimsical, and the characters are enjoyable. There is no need for overarching religious or romance subplot. It also does not take itself too seriously. Booster's Tower is an example of something so random yet so enjoyable about this game.
Too many RPGs these days are trying too hard. Everything is serious, everything needs a carefully crafted backstory. Plots are so complicated that you need data logs to keep track of it all. What happened to the RPGs where fun was the only goal? Where random purple octopi tormented the party? Where you can jump on NPCs' heads in order to get access to treasure? We've advanced a lot in terms of graphics, character development, and world-building, but we've lost that sense of whimsy that's so apparent in these 16-bit and CD games.
SMRPG had great characters, great platforming, and great adventure, and that puts it up there with some of the best RPGs of all time.