While CUDA is supported on GT 650M in the Macbook Pro Retina, it just meets the minimum requirements for the Ray-traced 3D Renderer.
After Effects sometimes complains that it cannot use the GPU for Ray-tracing. This appears to occur when other applications have used some of the GPU’s memory – quitting those apps (even a browser) and relaunching After Effects solves the problem for me.
I’ve read that since the last update in AE CC that this still an issue.
Other than that, as a mobile machine the MBPr is great.