Zack,
Take a look at this video I did in Motion. I think it is very similar to what you are after.
https://www.youtube.com/watch?v=OYm0d4VLvNw&feature=player_embedded
The majority of the files where created in Illustrator. Because I animated each “layer” or object I exported the file to photoshop. I then imported the layered photoshop document into Motion where I could work with each layer. I don’t feel like I lost any quality by doing that. The times I choose to work with the vector image is when I’m zooming into an object so I don’t loose sharpness. But in the case of the video the size of the objects does not change a whole lot. Plus, the photoshop files export out of Motion faster.
Zak is right, he is worth listening to and is very knowledgeable.
I think AE and Motion are similar and what you learn in one can be transferred to the other. So you don’t lose anything by learning one or the other. I think a lot of Motion users use both Motion and AE. Depending on where you want to go with your new skill set I think you will find that AE is the more widely used application. I used Motion a lot more because I feel it is faster.
PS. All of those images can be built directly in Motion by the way.
Hope this helps and best of luck.
Stephen Smith
Utah Video Productions
Check out my Motion Training DVD
Check out my Motion Tutorials