He has a valid point, but if you go for a vortech centrifugal supercharger or a turbo kit, your stock intake manifold an charge motion plates are retained. I believe in addition to the obvious features of the ford racing intake mani, it has shorter intake runners which are more conducive to a FI setup and make better top end power than stock. Not to mention it just looks great. I say do the ford racing intake mani. Cai's are plentiful used as well so keep that in mind.
06 GT, o/r x-pipe, magnaflow mufflers, airaid short ram.