Well as I said, the graphics should look the same in eSPXe, Mednafen and Duckstation unless you have some video settings changed or using shaders.
With 3D games you can up the internal resolution scaling with ePSXe, Duckstation and the Beetle/Mednafen HW core in Retroarch. This will make 3D games look sharper but 2D sprite based games with still look pixelated.