If you can afford them- both have their strengths.
Motion's
Fast and very easy to make changes- no rendering
Powerful behaviors much more flexible than keyframing
Amazing built-in particles and titling
Fast 3D effects
Lots of templates
AFX's
More complex and powerful compositing
More mature 3D system
Much more Plugins available.
Stronger compatibility with more formats
But as I said you can easily use both on the same project and at their prices I don't see why it wouldn't be feasible to get both + Shake too.
BTW- neither are truly 3D- that is extruded objects with depth. Both are actually 2.5 D- think of floating postcards in space. You have a camera that moves in XYZ space but you are dealing with flat planar objects. Though there are plugins for AFX that alter this somewhat. For true 3D you need Maya, LightWave, Cinema4D, Blender, etc.
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