No, really, this will fix 90% of issues with performance! What does this have to do with performance?
ONLY GUST AND KOEI TECMO effin KNOW! For some inexplicable reason both Sophie 2 and Ryza /2/3 might begin stuttering all over the place if they dont detect a controller. Also, they wont detect it on the fly. Exit, plug it in/pair it, go back in, problem might be fixed. The game might be stuck scanning for a controller in the background. Only god knows.
You can also use a software to simulate a controller.

https://drive.google.com/file/d/1ZtCoky-X15ZuUFXo2F6VCMh8ZMXSELUf/view
Drop the .dll in the same folder as the game's .exe

This is a windows version of the fix made for linux, recompiled to work on Windows by TellowKrinkle
https://github.com/TellowKrinkle/atelier-sync-fix/tree/windows

Based on
https://github.com/doitsujin/atelier-sync-fix for Linux

Reports say it works better on windowed or borderless fullscreen with vsync on

Always set the game to FULLSCREEN
Motion blur makes the camera jerky, I recommend turning it off.
TAA doesnt work. It's better to turn AA off entirely and choose a higher resolution than your monitor's if your pc can handle it. Keep in mind 4k is absurdly demanding on gust's engine so even in a pretty good pc 1440p might be the sweetspot.

If you experience a sudden drop of performance try alt-tabbing or changing to a lower resolution and then changing back to "refresh" the rendering (from StabbyStabby)

Enter your driver's control panel and:
Enable Low Latency to Ultra
Set framelimiter to 60 overriding the games broken one.
If your pc cannot handle 60 fps, set vsync to half and limit fps to 30 with no vsync
If all fails, try setting priority for the game to realtime in task manager and Set to maximum performance in energy consumption in the Driver Control Panel

DO NOT USE THIS ON WINDOWS
Use the latest PROTON-GE or Proton Experimental
Download this file https://github.com/doitsujin/atelier-sync-fix/releases AND EXTRACT
Put d3d11.dll in your game's .exe folder
Paste
WINEDLLOVERRIDES="d3d11=n,b" %command%
in your game's launch options under properties to activate the fix.
This fix also works for Ryza 1, 2, Sophie 2, and the Mysterious Dx Games
Set the resolution to 720p (fullscreen option stretches) and use fsr
Recommend leaving most settings on low preset, except textures which can go to standard, and setting bloom, dof, ssr and light shafts to on to make it more presentable. Play with the settings, but only AFTER doing the steps above.
Be mindful of the fact Atelier games like to reset settings to a default (which is way too high) sometimes so always check on launch. You can help the game remember settings by exiting properly by quitting from the game instead of the steam overlay.

For people who want to get rid of the black bars, modify this file:

/home/deck/.local/share/Steam/steamapps/compatdata/1999770/pfx/drive_c/users/steamuser/Documents/KoeiTecmo/Atelier Ryza 3/Settings.ini

and edit these two lines:

ScreenWidth=1280

ScreenHeight=800