CrossCode! A modern topdown action RPG with gorgeous pixel art, great music and Zelda-like puzzles in dungeons. The full version is available for PC, PS4, Xbox One and Switch and there is a demo that you can play in your browser.

Disclaimer: I'm friends with some of the devs but I would still recommend it if I wasn't.

Baba is You - simplistic graphically, but immensely satisfying mechanically. Amazing puzzle game.

Celeste - gorgeous graphics and buttery smooth controls, a platformer that is encouraging and supportive all the way through but ranges from "easy as pie" to "hard as nails" as you progress. One of the most satisfying games to complete every level for. One of the best soundtracks ever. Trans rights!

Fez - another simple-ish at face value platformer game, but this time with puzzles as the main thread instead of action. Super satisfying puzzles and an amazing soundtrack.

Omori - an RPG which eventually deals with some heavy subject matter but does so tastefully and maturely. It's a splendid story either way you spin it, and lots of fun.

Undertale - same as above, but shorter and more "punchy". One of the best soundtracks in gaming, and a cast of characters you'll come to feel like your family. It's quite subversive for the genre, so it's a fun experience. It has an episodic sister game Deltarune which is still in the works.

Void Stranger - a block-pushing styled game, but incredibly subversive for the genre. Gorgeous visuals, great soundtrack, and some truly mindbending puzzles. It gets super hard, but it's also super satisfying to beat.

Stardew Valley - cozy farming game, really just oozing passion and love from the developer(s). Lots to do, many unique people to meet and things to see. Pretty graphics and stunning soundtrack. Fall in love with an NPC, marry them if you want. Or don't do any of that. Make your own fun in this one, there's a bunch of aspects to get into.

Citizen Sleeper - not technically 2d but may as well be. A gripping, beautiful sci-fi story, told in a tabletop RPG style. You won't be able to help falling in love with the rag-tag character cast, and shedding a few tears along the way. It's very down to earth but makes me long for the stars at the same time.

Ori and the Blind Forest/Ori and the Will of the Wisps - a drop dead gorgeous, lovingly crafted metroidvania with one of the best soundtracks you could ever ask for. Platforming is gorgeously refined, and the sequel improves upon the first game in many ways.

Hollow Knight - I could copy paste the majority of the Ori blurb here, however this game has a deeper focus on the deep, winding, sprawling exploration, and combat aspects. Gripping soundtrack and stunning stylised visuals. You will, however, join the wait for Silksong with the rest of us, which drives many people mad!

Sundered is a cool 2D metroidvania / action rogue lite blend.
Absolutely gorgeous artstyle, unique concept..

Loop Hero is another rogue lite, that has a bit more of a management feel to it. The hero traverses the loop (the level) automatically - you just get to change their equipment and the environment. It's a cool balancing act between making a tough level with synergetic enemy types/tiles and making sure your hero survives.

Hollow Knight - if you like metroidvanias you probably know that one. It's incredibly popular! amazing game.

Dead Cells - same basically :) 50% off on steam right now!

Edit: Seems like you're looking for retro/emulation stuff mostly? I might be misunderstanding your comments.
These recommendation all have Switch and PC versions. No clue how well they would run on yuzu

Terraria. It has RPG elements and is simply fantastic. Often available at a discount on Steam which I only recommend due to the extensive content available via the Workshop.

Hyper light drifter

Bahamut Lagoon is a cool JRPG for the SNES that sadly never was released for the west. You can get your hands on the ROM and some fan translation though. I've played it many years ago, so my memory's a bit iffy, but I do remember having a good time.

Front Mission is another good JRPG entry from the 90's. I loved the SNES version, but apparently the DS version boasts extra features and content, making it the superior choice.

Hollow Knight

/edit: SteamWorld Dig 1 & 2 are also very good metroidvanias.

Have you played Dead Cells? It's a great metroidvania

If you like Pokemon, check out cassette beasts. Or one of hundreds of Pokemon mods.

Hollow Knight and blasphemous are a couple of great metroidvanias and also a pretty good challenge.

I liked Metroid Dread a lot. I feel like it's a good starting point for Metroidvanias too because the game does a good job nudging you in the right direction e.g. by closing off certain areas but still letting you explore and figure out where to go. I especially enjoyed the movement, it feels very fluid and satisfying.

The only major issue I had with the game was that performance is really bad in a few encounters. Most of the time it runs fine though. It's also not super long. I prefer a game that doesn't overstay its welcome, but if you're looking for something that is good value for money in terms of playtime there might be better options.

Been just thinking about one of my favorite SNES era games -- Illusion of Gaia. If you're doing emulation, highly recommend. I'm in the process of picking up a SNES and functioning cart to play it myself for the first time in a decade.

Axiom Verge 1 is a great metroidvania. I also tried 2, but it didn't click with me at all. Cave Story is great as well. Dead Cells, but that's more of a rogue lite game. Binding of Isaac is also one of my favorites, but it's a top down rogue like.

If you want an indie game dev suggestion, Ojosama makes a tonne of great games on Itch.

https://ojosama.itch.io/

Ghost 1.0 It's an indie game much in the style of older games, and it's made with love

Signalis is a 2.5d top down 3rd person single player survival horror title available for switch, it is probably one of the best modern examples of the genera taking clear inspiration from older titles like silent hill and resident evil 2. It’s very story based and currently on sale for the switch, I would highly recommend it.

It is a new game, but it very much has an old school vibe and is clearly leaning strongly on what made older titles great.

Obligatory short list of great old school RPGs:

Fallout 1 & 2

Baldur's Gate 1 & 2

Icewind Dale

Planescape Torment

(I think Neverwinter Nights belongs on the list as well, but I can't attest to it as I've never played it.)

You can pick up most of them from GOG.COM for cheap.

There should be enough to keep you occupied for a while.

I have been playing the absolute shit out of StarSector. It's part OG space trader, part 4X, with a great battle system and a vibrant moding scene. It's affordable, and will run on just about anything.

Maybe a dumb suggestion, but since you mentioned older systems, Castlevania: Symphony of the Night is a PS1 classic that helped create the Metroidvania genre. There's also Bloodstained: Ritual of the Night, which is a spiritual successor by one the key developers behind SOTN. Dead Cells and Hollow Knight are solid games that have been recommended already, but if you find yourself enjoying the rogue-lite elements of those you might enjoy Cult of the Lamb. Admittedly it's top down 2.5d, but it's a nice blend of rogue lite and town management as your tasked with building up a cult and turning it into a thriving community in between fighting your way through dungeons.

First game has been mentioned already, but I wanna make sure it's clear how singular the game is.

Blasphemous. In case you didn't check it out: You should. It got multiple major updates (new areas, bosses etc.) that were completely free and sometimes you can grab it on sale for as low as 6€. It even has NG+ only content for replayability that's actually worth it (trust me, it really is). The movement in this game is beautifully smooth and the pixel art is consistent. More importantly the combat is actually excellent unlike many other metroidvanias (as well as souls-likes) that unfortunately fail here imho. The platforming is unique, but relatively easy to learn (but you need to try), although the game has specific areas where it becomes more or less important. Blasphemous 2 also exists, however I haven't played it yet. It isn't as hard as Dark Souls titles or so, but it's a souls-like that won't go easy on you at some points. OST by Carlos Viola is also nice for people who like themselves some flamenco style.

If jRPGs count: Chained Echoes. I will never shut up about this game, since it has gotten a lot of attention, however not NEARLY enough... no one seems to really care about it anymore, but it's one of the best games I have ever played and I feel sad how it has been overshadowed by games with better marketing/higher budgets that weren't comparable in terms of gameplay or charme at all! It has everything: Awesome gameplay with many QoL features to adapt to the game or adapt the game to you, cute and profound character designs/artwork, a storyline and an AWESOME OST! Honestly, the music is beautiful in this game... the game has been made by one guy only, however you won't notice that (except with occasional silly bugs). The music has been made by someone else though (Eddie Marianukroh) and with the help of some awesome musicians (like Gregory Orosz aka. Gamer of the Winds). I wholeheartedly recommend giving it a try!

Not a Metroidvania game but I had fun playing ASTLIBRA Revision last year.