Yeah must be the cam. I just looked up the specs...
L99:
Valve Lift (in): .500" intake/ .492" exhaust
Camshaft duration (@.050 in): 195 degree intake/201 degree exhaust
LS3:
Valve Lift (in): .551" intake/ .522" exhaust
Camshaft duration (@.050 in): 204 degree intake/211 degree exhaust
This would definitely account for the power difference - especially on a FI car. I think the VVT of the L99 is a good idea, but after having the AFM for around 8k miles and having it tuned-out for 2k, I'd say it's more of a hindrance than a help. Kind of wish the A6 came with the LS3 but oh well, I have no problem turning a wrench or two