well other then the FMX being a bit heavier then the C6 and slightly harder to get rebuild parts for there is no difference, in that the gear ratios are the same.
the car might be 50 pounds lighter. they say the C6 is less efficient then the fmx. I've read guestimates that claim a 55-65% Drivetrain loss with a C6 and claim 45-55% loss with a FMX.
I know that the FMX can take a lot of power as well, not as much as a built up C6 but i've seen people with FMX transmissions holding 450+ HP no problem.
People tend to go with what is known, the c6 has proven itself and has a larger aftermarket following in support.
the FMX you can rebuild it but that is about it. there is no shift kits or upgrades for it.
i'm on the fence, at some point i'm going to have to ditch my C-6 for either another C-6 or a FMX
If i go back to a FMX i have everything i need. As for the C-6 i'm still missing some of the correct parts for the shifter lockout, also if i went back to a FMX i would have to change out my driveshaft.
so i don't know, its really up to you, if you car is running and everything works, i would just leave it be, why have the headache the trans won't blow up with 350hp, if your taking it to the drag track or road course once a week its another story.