Here's a general breakdown, pretty much lines up with Bosscat's remark:
C4:
Weak in stock form.
Can be built very strong.
Dollars invested = Strength
Compact
Light
Lowest parasitic power loss.
No mods to driveshaft if swapping between FMX
Best aftermarket support.
C6:
Strongest in stock form.
Very heavy
High parasitic HP loss.
Need to shorten driveshaft if swapping from FMX or C4.
Big, bulky
Good aftermarket support.
Many headers interfere with the tranny due to width.
This may or may not be the case with your car, depends on year, header, engine family, etc...
FMX:
Cast iron, so heavy tops the list.
Least aftermarket support.
Some cast iron internals are fragile.
Swaps easily with C4.
Was designed in the mid 50s.
What year car.
If it came with an FMX, it likely will fit a C6 fine.
Some cars it is a tight fit though, and some cars may require tranny crossmember mods.
Edit: Just saw that you likely have a 72 Stang
Being a little bigger car, you would definately want to build a C4 strong. The C6 will swap in with a little driveshaft surgery.
Have you considered an AOD?
They are weak also in stock form, but should be built strong anyway before use, just like the C4.
Someone will correct me if I am mistaken, but I believe it would be an easier swap than the C6 just due to the driveshaft issue. The AOD should take to the FMX/C4 driveshaft fine.
Anyway, the AOD would make the car a much more street friendly cruiser with the OD.