Maybe the Mass Effect games? The first one is the only one with “loot” and the tactics aren’t very complex for the most part. The story is very good and the world won’t feel empty since the games are more linear. If you find the first game isn’t to your liking, try skipping straight to the second one. They streamline a lot of the mechanics after the first game.

Disco Elysium lacks grinding and battles but is very much a roleplaying game with a compelling story and characters (including those in your head).

Crosscode is an ARPG which will certainly scratch that itch for Zelda like dungeons. Combat is skillful, but easy enough that you don’t have to grind out the best gear and levels, though there is the option to grind a lot if you were to want that. The story is also really nice.

Crystal Project is the best JRPG I’ve played in a gameplay sense but it will require you to level classes and consider abilities. The reason I’d recommend it is because combat isn’t really just bigger numbers, end game combat encounters especially are like puzzles where you need to use the right tools in the right order. Also I’d say half the game is about exploration, the game embraces sequence breaking and going your own way, and has fun though occasionally frustrating voxel platforming. If you want a JRPG that is more story focused then I think Mario RPG is great, and you don’t have many choices to make as there are only like 5 characters / classes, it also has some voxel platforming and comedy.

This is a difficult one to answer as most RPGs I can think of have some combination of the stuff that puts you off. Have you tried the Witcher 3 (great story, and the RPG elements are fairly simplified) or Deus Ex: Human Revolution? And if you’ve played Nier Replicant and enjoyed it, I think you’d love Nier Automata.

If you’re into FPS games, here are a few suggestions that have RPG elements:

• Deus Ex
• Borderlands
• Bioshock
• FarCry (#3 and after have progression elements, not so much for earlier entries)

Dragons Dogma - great action RPG, leveling up is automatic, you buy abilities and just assign them to your action slots. You can change vocations(classes) anytime without much penalty and it’s one of the few games where magic feels brutal and mages are super deadly, but all classes are fun to play.

The combat is something between Dark Souls and Devil May Cry and you can interact with all monsters: climb on large enemies, grab smaller foes, grab flying mobs, etc

The story is probably the weakest side, as it’s not very clear what is going on for a while, but once you piece stuff together it’s truly amazing, especially when you reach the endgame and beyond.

You can pick it up for a few euros/dollars as it’s often on sale.

Super Mario RPG: Legend of the Seven Stars might work. It’s going to be difficult (fear the spear) and you’ll want to use those items, but it is overall easier than Chrono Trigger. And it has a remake coming out soon with some system changes.

Final Fantasy Mystic Quest was intended for your situation, but it’s balanced in all the ways you dislike.

Otherwise, possibly the very easiest remakes of old games like the Final Fantasy 4 Pixel Remaster.

I really liked the Yakuza games. They’ve improved a lot over the years, the story is engaging, and there’s tons of fun side stuff to do. Although the audio is all in Japanese, so you have to read subtitles.

It’s a bit of a long shot, but you might enjoy traditional roguelikes. At least, I kind of felt similar and then found them to be what I was looking for. How they fare for your individual points, roughly sorted from pro to not-necessarily-pro:

• I don’t like the feeling of being OP, I want to struggle through the end
• I hate grinding

Traditional roguelikes have brutal difficulty and grinding is effectively not a thing you can do.

• using items feels like cheating, so I tend to just use character abilities (I will heal if needed); I’d rather “git gud” than buy and use items
• I don’t like loot

The brutal difficulty forces you to use items. It won’t feel like cheating, but rather the only way to progress.
And there’s no way to sell loot, so basically whatever you find, either it’s new equipment or you just leave it there.
This also means money is extremely tight. You won’t be able to buy a hundred cheese wheels to counter-heal through encounters.

• turn based combat (tactics) is generally boring, but I do like puzzles, so that can make it acceptable

Very much turn-based, although not JRPG-style (which I dislike, too) and the games do generally feel like large, somewhat less strict puzzles.

• I don’t care about leveling up/character builds, it feels like a chore; abilities also don’t interest me

Well, this one’s a bit tricky. Traditional roguelikes are kind of all about that, moreso than RPGs. Because a death (or a win) resets your game progress, they can rapid-fire progress at you.
On the plus side, this is all part of the larger puzzle. It is not just a chore, but rather key to beating the difficulty.

I guess, I should also point out that by “traditional roguelikes”, I mean games that are actually like the 1980 game Rogue. So, don’t expect hyperrealistic 3D graphics. 🙃

Here’s two games that are relatively popular + beginner-friendly:

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For Chrono Trigger, that fight with Magus is a two-phase fight, and you’re not underleveled unless you can’t get through the second phase. Since you’re pinning it on RNG, it sounds like you didn’t make it to the second phase. The first phase is on the tactical (or puzzly) side and it’ll punish mistakes, which catches some players off guard. A change in party could possibly help too, depending on who you’re using. If Lucca’s in the party and you’re not using items, that fight’s probably going to give you a bad time.

Anyway, my top recommendation based on these criteria is Terranigma. It’s an ARPG with a very basic equipment system and you can go through the game only using HP restore items. The difficulty curve is fairly tight, with just a notorious level requirement later in the game. Try not to be put off by the script; it’s messy in places due to a very small Western release, but the underlying story is great. You could also try its predecessor, Illusion of Gaia, which has fewer RPG mechanics (it’s more like a Zelda game).

Other than that, I’d recommend trying to finish Trails in the Sky. Sky FC doesn’t show its hand until late. That–still ongoing–series is doing something with its story that isn’t being done elsewhere in RPGs, and it’s very rewarding if you can successfully connect with it. You’ll also probably enjoy the combat more later in the series.

If on your Ys journey you haven’t made it to Oath in Felghana or Ys VIII: Lacrimosa of Dana, those are very popular in the fandom, and Ys VIII was a little bit of a breakout hit for the series for newcomers. Celceta isn’t very good.

A few games that I think you might like based on your post:
Cult of the Lamb
Dark Messiah Might and Magic
Drake Hollow
L.A. Noire?
The Looker
Pony Island (you like puzzles right?)
Red Faction Guerilla
The Aquatic Adventure of the Last Human

Also metroidvanias as a genre are probably a good fit for you.

Try CrossCode! It’s action based so it won’t feel too RPG-y.

The story is really good and the characters are extremely well written. At the risk of sounding cliche, they’re so well written they feel like real people.

The dungeons have puzzles which you may enjoy since you like Zelda games.

The combat is really fast and skill based, and you respawn immediately at the last door you walked through, so you might find this gameplay loop rewarding since you like Souls games.

You don’t have to grind, but if you do try this game, try beating a bunch of enemies until the S rank bar appears. Something fun will happen :)

Have you tried Outward? It’s not the world’s prettiest game, and it is a bit clunky, but I loved it.
It definitely sits somewhere in the Morrowind-Soulslike-Zelda-ish genre you’re after.

If you like soulslike, I recommend The Surge and The Surge 2. Don’t need much grinding, the environments are nice and the combat is sharp.

Have you looked into the Batman Arkham series? They have great stories, and feel kinda Zelda in that you get new tools as you progress. There are puzzles which I don’t always love, but maybe you do.

There is combat, but you can play on easy. And you upgrade your skills, but it is not very crucial to the experience.

And also maybe portal? Not very rpg, but environment changes as you progress.

Try Sea of Stars, it scratches that Chrono Trigger classic RPG itch, while nearly completely eliminating the grinding. I got every achievement in it, and at no time did it feel like a slog.

• Wanna get every item? There’s a feature that facilitates that, which lets you know what areas still need to be swept, near the endgame.

• Feel like you’re not leveling fast enough? There’s an easily purchased in-game item to double XP (toggleable)

• Only got time for short sessions? Save points are everywhere

And yet, the game isn’t too easy, either.