On which games do you notice the slowdowns?
The downside of batocera is the lack of DirectX support (because batocera is based on linux and therefore there is no possibility to use DirectX, which is only available on Windows machines).
At the moment only OpenGL is possible in batocera (maybe someday Vulcan).
Some PS2 games may run better on Windows with DirectX than on Linux with OpenGL.
And i guess that is your issue :(
You could alternatively try your ps2 games on Windows and you could use Retrobat for that: http://www.retrobat.ovh/