Motion is for
MOTION GRAPHICS
AE is for
AFTER EFFECTS.
Let me splane:
Motion works on the principal of creating graphics and animated texts etc (though LiveType is still better in that respect, but they are bridgeable between the two anyway) using ALOT of your GPU to render the stuff.
its workflow is AWESOME for creating quick slick looking graphics for say commercials, newspots etc.
it can crank out stuff lickity split, whereas AE takes ALOT longer to do the same thing because of the way AE works with layers. Which in ALOT of cases is far superior. but when it comes down to professionals needing to create a TV spot in less than half a day, Motion is the best for it. There arent "behaviors, presets" for AE like there are for Motion, and in essence it makes things quicker, sometimes.
BUT it is NOT a video editor in any respect of the word, it creates more than edits video.
After Effects is just that. Use it AFTER you have cut your videos etc to add effects.
After Effects can do TONS more things than Motion, but you arent going to be cranking out any completed work in nearly half the time of a Motion workflow. I havent used Motion much because I dont do those kind of motion graphics (and when I do, LiveType suffices).
IMO Motion is LiveType plus the ability to do from scratch motion graphics and control them better.
LiveType is AWESOME, but its interface sucks and is missing ALOT of right clickable menus etc that Motion has.