Wow, I've actually played through 7 of the top 20.
Dark Souls, Dragon's Dogma, Chrono Trigger, Nier Automata, FF6, Mother 2, Dragon Quest 3
Well, that's kind of a lie. I never bothered with the last boss of DS, and I never finished FF6 and I cannot for the life of me remember if I finished DQ3.
I also voted for none of them. My thoughts:
Dark Souls is at least some kind of local optimum when it comes to game design. Gamers I respect have described it as a perfect symbiosis of RPG and action. I disagree, as IMO any perfect symbiosis would require reconciling "numbers go up" with player skill such that players can't avoid checks on the latter by abusing the former. In practice, grinding may be so boring and lengthy as to be avoided by almost all players, but in Dark Souls this is not the case. Also, as far as the action goes, it's very good, but far from something like Ys Origin and Oath in Felghana, especially when comparing boss fights. In comparison with those games, the Dark Souls dungeon (or world or whatever you want to call it) is far more challenging to navigate. Nevertheless you soon learn there's ways to avoid almost all the challenge here too, so in order not to cheese the game you have to make a list of house rules, or simply start larping. What's left is what I call a "mood crawler", specifically a single character action mood crawler, and from this perspective it made some welcome design trade offs against its predecessors, but didn't fundamentally outgrow or overcome the contradictions inherent in Action RPGs.
Dragon's Dogma is a 3D action sandbox. Like most action RPGs, there's little challenge to be had if you're playing to win. Instead you'll get the most mileage by exploring the move sets and numbers till you find something that you think would be fun to take through one or more of the dungeons, and then doing exactly that. I think the designers were very conscious about this being the way some people would approach the game, and put a bunch of game changing but obviously suboptimal equipment in one of the shops for players to play with. I deliberately played very underpowered.
Chrono Trigger I finished when I was a teen and haven't played since. I have fond memories of it though, and I do remember finding every other squaresoft RPG I played after lacking in comparison.
Nier Automata I absolutely loved, but more for what it tried to do (glue a bunch of arcade genre action gauntlets as well as Devil May Cry lineage 3D action into an overarching Ocarina of Time structure with Souls bonfires thrown in) than what it accomplished, and of course for the world and art. Objectively speaking I can't rate it as very good, aside from like Dragon's Dogma, a sandbox.
Final Fantasy 6, like Chrono Trigger, I played when I was a teen, but also again more recently when I was in my 20s. It's actually quite well done. Well paced with good character selection based blob combat menu customization (as opposed to more explicit menu customization ala FF5 classes or FF7 materia). I can't remember if the encounter design was as strong or stronger than FF5. Could be a decent experience if you play it in a semi-speedrun way.
Mother 2 isn't great. It's entertaining as a cultural artefact, but as a game it's quite bland. Mother 3 is better as a game, has a similar brisk pace to Phantasy Star 4.
Dragon Quest 3 is often used to show "see JRPGs can have classes and character creation too!" but there is a very obvious optimal party (bunny girls, IIRC), and the encounter design and content don't really make it very entertaining to go for anything but max power and blast your way through it.
Bonus: I didn't put a lot of time into PS1 FFT, but I did complete FFT:A on the GBA, BitD, and I didn't like it at all. Gets the SRPG genre very wrong. From what I can tell, so does the original.
I also played a bit of Lufia 2. Fun Sokoban like puzzles, but probably better to just play some puzzle game.