Fx3S has 2 SD/MMC card slots which sacrifices 16 data bits from the GPIFII interface.
Apart from that, the two chips are the same.
Choosing between the two chips would depend on what exactly you are interfacing to the Fx3(S).
We want to use EZ-USB FX3 with external processor. External processor will be the main processor of the system.
How to interface EZ-USB FX3 with external processor?
Do you need the SD/eMMC slots? If yes, use Fx3S. If not, use Fx3.
Either way, you would likely be using the parallel port (GPIFII interface) to communicate with the external processor.
You can design this interface as per your requirement using the GPIFII designer tool and creating a state machine based on external/internal signals.