My personal/optimal configuration to run all games at stable FPS:
Always CHD and european versions (PAL games run better but i can't remember the reason in this moment)
Inside Quick menu:
Core options > Video > Threaded Rendering Asynchronus
Core option > GPU Plugin (advanced) > All On except for "Hi res downscaling" (for certain games like bloody roar 2 it is necessary to have it activated because otherwise it has graphic errors that are solved by activating this option and also does not lower the resolution too much, which is strange, but for all the others I do not recommend it because honestly, although they reach 60fps easily with it, they look horrible.)
Core options > Audio > Reverb effects Off, Sound interpolation Off, all the other options On
And no more. the rest is not necessary to touch it although you can try to get a couple of extra FPS
In the newest version there are some extra options in the sections of quick menu but that versions are the ones who for some reason just run worst.
of course, this configuration is on a new 3ds, I have no idea how it will be on an old one.