The only thing you will be missing is the CUDA accellerated ray traced rendering of extruded shapes and text and bent layers in AE. C4D lite will work just fine as well as all other effects. Todd has posted comments about this several times in recent weeks.
Until someone has one of these new machines in their hands everything about performance and capabilities is pure speculation. There is no PC available yet that uses the same processor or GPU to compare with the Mac Pro. Everything about this new MacPro so far is pure speculation.
As Rick says, the GPU acceleration of the ray-traced 3D renderer is the only thing in After Effects that requires an Nvidia GPU. Every other GPU feature works fine on AMD cards.