I'm going to make an educated guess that Motion 3 will work a lot like Motion 2, and having worked on plug-ins for Motion 2 (which will also work with Motion 3), I can say that Motion, and FCP both use premultiplied alpha. In my experience with compositing in Motion and FCP, I'm inclined to say that AE is still a better compositing tool.
For other things, like particles, live fonts, and such, Motion may give you better, realtime feedback than AE. As a result, it may give you a faster workflow for colorful effects. I think it's going to come down to which environment you like to work in, and what sort of work you do. If you're mostly compositing, I think Shake or AE are where you want to be. If you're doing a lot of motion graphics and you like Motion's interface, then it may be something to consider.
Of course, if price is no option, get all three!