The main reason I'm planning on using After Effects rather than Motion is the wealth of information and tutorials there are for it.
One example is Lightsabers. I think I did a search for how to create Lightsabers in Motion but there were a few different methods and the results didn't look that great IMO (though there was a great tutorial on how to create them in Shake, which is now discontinued)
After Effects on the other hand has a wealth of tutorials on it, most notably the one on Videocopilot, where they're even nice enough to supply you with their own presets.
It's not just about the lightsabers though. There are other things I plan to try out, but have only found tutorials for how to do them in AE.