It all gonna depends on what you are trying to achieve, the PIC you are using, the amount of resources required and the required features.
FatFs is quite popular, you might get support from many forums and it regularly maintained. It’s main advantage, it can be used by a variety of microcontrollers, not only the PIC.
Microchip MLA could be simple to use as it will fit easily together with other microchip tools like MCC but at the moment it does not support 8 bit microocntrollers like PIC16F and PIC18F series only 16 bit microcontrollers.
You an try both and see the one that will work for you.