The main difference is that Motion doesn't have a 3D camera or 3D lights,
so you'll have to use the ones supplied by the 3D Flag plug-in. The
3D Flag camera/lights should be sufficient for most of your needs.
If you have both Motion and AE then I'd say the choice comes down
to determining which package you'll be using to integrate a flag into a scene.
If you do most of your work in After Effects, then the AE version is a good pick.
Otherwise, Motion should work for you.
I've downloaded both demos and am able to get something out of AE with it. The Motion one gives me pause though. The only manual I could find was the AE one. While Motion overall is not that complicated, I tend to 'think' in either an AE or Shake mentality. So, I guess it's the AE version.