I was a huge fan of motion until I started doing some pretty heavy projects. Then it turned out that after effects actually used the ram that I had installed.
I read somewhere that motion is limited to 1.5gb RAM or something like that (sorry for my ignorance!) were as after effects isn’t.
At the same time I had to go on a course to understand how to use after effects so it depends on what your doing and the time you have.
I have been using After Effects for about a year now and before that I was solely using Motion for about 5. I really feel like I was blinkered with Motion and almost like trying to do everything in the language of Apple. With After Effects its like my native language and it makes sense to me to do it that way.
My advice is After effects all the way.
Good luck!