I think the biggest differences between stock and aftermarket is takeup points and how stiff the pedal action is. The other major difference is most aftermarket units are "rebuilt" and will probably not last as long as OEM.
I think the OEM will handle most forced induction mods out there right now. It really depends on what you are using the car for. Drag racing (or street racing) would be better served by an aftermarket unit. Personally, for street use or road racing circuits and the ability to match revs (heel and toe), any of the available units will work.
Just for comparison, I have the OEM in my street car, which was run on the track my first year of experience. My present track NSX has the Dali ACT clutch. Slightly smaller "sweet spot" and much quicker take up. Whereas the OEM unit does not engage until the pedal is almost all of the way out, the ACT unit engages almost as soon as you start releasing the pedal, which is nice at the track. HTH.