RPG is my favorite genre ever.  I've played hundreds over the years. I like so much. I love many I have played. I wanted to make a list of my faves. To keep this list manageable I avoided some sub-genres like side-scrolling RPGs or beat em up RPGs and such like Guardian Heroes, Dragon's Crown and the like.  You can include whatever you want. I'm just going to stick to more traditional RPGs for my own benefit. I even skipped some WRPGs as I feel that could be its own list. Again you can list whatever sub-genre or not.

Ys 1

I don't know why I love this game so much but I do. The opening on the Turbo 16 CD gives me chills every time. Yuzo Koshiro's music is amazing. On paper, this game sounds like every other RPG. The teenage boy saves the day from an evil ruler. There is just something about the combination of music and atmosphere that makes this feel like a grand and fun adventure. Not to mention the speed of this game. Ys series plays fast and furiously. A short game as well. 6-10 hours. This game is quietly one of the most ported and remade games in history. It's been ported and remade on more systems than I can count. The best remake is on Steam with Ys Chronicles.

Grandia 1/2

These IMO are some of the better RPGs of their era but got overlooked for being on SEGA consoles and then poor ports on PlayStation systems. Grandia 1 has one of the best main themes in RPG history. It's up with Skies of Arcadia as the best sense of adventure an RPG has ever had. English version has some of the worst VA in history tho. Grandia 2 is a little darker game in tone but still great fun with great music and enjoyable characters. It came out a year before FFX and at the time considered the best looking RPG ever in 2000 lol. Grandia II improved on the VA as well. Hiring mostly Metal Gear Solid Actors.  Jennifer Hale( Every game ever). Cam Clarke (Leo/Rocksteady in TMNT/Liquid Snake in MGS). Paul Eiding(Roy Cambell in MGS). Jodi Benson (Ariel in Little Mermaid) Grandia II may not be the most original but it has a lot of charm and strong performances in well-done characters. On Switch now.

Skies of Arcadia.

One of the best RPGs ever that no one has played.  No game has taken place in the clouds as fun as this one. This game is not one you play for the story. It's very simple. What it does have is a real adventure feel like pirates. Energetic cast. Fun as hell ship battles. Fantastic music. This your fave Saturday morning cartoon as an RPG game. Sadly it's only on Dreamcast and Gamecube and quite expensive. An emulator is the best bet right now.

Final Fantasy IX

This is my fave FF game of all time. The themes. The music. Story and characters. Art. You name it. I love it...except the tetra card battles but that gave me as trouble as the battles in FF7 Gold saucer so whatever. For every reason this is Sakaguchi's fave FF it is also mine. It feels like the purest form of the soul of what FF is supposed to be. That is coming from Sakaguchi and I agree with him.

Xenoblade 1/2

The scope and imagination of the unique setting to this series are amazing. They are well written. I care deeply about the characters. Monolith is possibly the best at world-building narratives. I'm super hyped to play the remake next month.

Final Fantasy VII

Nothing I can say that has not been said. It's a great game tho some parts have aged like trying to figure out where I am to navigate pre-rendered areas.

Tales of Vesperia 

Only Tales game I ever liked and I adored this game. In many ways, it reminded me of Grandia II. If you play 1 Tales game this is it. Yuri is one of my fave JRPG protagonists ever. He really breaks a mold. He's not spunky. He's not a teenage silent orphan or only has his mom. He's not a dark edgelord either. He's really well done.

Persona 4 G  

P5 may have a slicker presentation but IMO P4 has a better story and cast. I feel this has a better sense of comradery. I feel their hurdles are larger. P5 is "cool" where P4 feels they really are overcoming something huge. A string of murders. More complex characters. I love every Persona I played this stands above all IMO

FFVI

Again not much can be said that has already been said. One of the best RPGs of all time. Possible the best FF game ever made.

Chrono Trigger: First RPG I ever played, and still one of the greatest games of all time.

Final Fantasy IV: Amazing story, great soundtrack, and my favorite cast of characters of the series.

Breath of Fire II: My favorite BoF.

Super Mario RPG: Still the best Mario RPG ever made.

Final Fantasy VII: Probably the best RPG on PS1.

Final Fantasy IX: The first one I played on PS1, still a great game.

world of warcraft

Xenoblade-  To me the perfect balance of a story being complex with a lot of twist and turns and room for the gamer to figure stuff out without drifting into the convoluted and wacky.  Also balances MMO like style with a large open world and tons of optional grindy sidequests but with a compelling main storyline.

Pokemon-  They're cute and the battle system is great.  Games are mostly interchangeable to me.  

Skies of Arcadia-  Mainly because of the reasons mentioned by the OP, but I think they're selling the story short.  Essentially it's a tale of two naive children being dumped into the world, one seeing the best humanity has to offer and one seeing the worst.  

Tales of Symphonia-  Classical RPG tale of chosen hero needing to find x macguffins to save the world from destruction.  But what it does it does incredibly well.

Paper Mario 2-  Best of the Mario RPGs.  Great script that is constantly amusing, and does an amazing job of giving you various scenarios to keep things fresh like becoming a wrestling star and solving a train mystery.

Final Fantasy 7 : first Jrpg I have ever played. Up to this day somewhere on top, certainly with the bliss that is called the Remake... It's so damn awesome!

Xenogears : Fantastic and captivating story, disc 2 anyone?

Xenosaga : Another Sci-fi bliss. Story rules, Gnosis, I got ID!

Shadow Hearts : Great setting and again, story and gameplay were loads of fun.

And then some... 

Lunar SST, Wild Arms 3, Star Ocean 3, Arc the Lad Tots, FF 6-X...

Witcher 3
Dragon Age Origins
Legend of Dragoon
Divinity: Original Sin 2
Jade Empire
Star Wars: Knights of the Old Republic
Elder Scrolls IV: Oblivion
Mass Effect Trilogy
Path of Exile
Gothic 2
Deus Ex

Xenogears is amazing.  I was never so happy to spend 90 bucks on a CD soundtrack

I think it's a tie between Nier and Chrono Trigger for me.

Other honorable mentions: Persona 3, Persona 5, Nier:Automata, FFVI.

Damn, you're ugly.

Chrono Trigger
Final Fantasy 6, 7 and 12
Breath of Fire 2 and 4
World of Warcraft
Nier Automata
Bloodborne
Witcher 3
Dragon Quest 6 and 8
Suikoden 2 and 5
Ogre Battle 64
Super Mario RPG
Ni No Kuni 1
Seiken Densetsu 3
Vagrant Story
TES: Skyrim and Oblivion
Diablo II
Ragnarok Online
Grandia
Valkyrie Profile 

A bit of a long list, but this is my favorite genre and all of them have been at one point in time amongst “my favorite games of all time”. Most of them still are, they made my "top 50 games ever" recently. I’ve replayed them multiple times and in some instances it takes a bit of effort to even stop playing them (WOW specially).

Have a couple more in mind but I’ll leave it as it is.