I need to create a stop motion animation for a client...
It is basically a scene where a bunch of pens and markers draw out a scene on a piece of paper.
I'm thinking that the paper could be a real drawing that I scan in various stages of the drawing.
The markers and pens could be 3D rendered models rendered out at 5 or so frames per second individually so I can adjust each as needed...
I think the way most people approach this, if they don't just do it all in Lightwave or Maya or something like that, is to do it in AE, by recording the path or strokes of the words being written, say, with a wacom tablet, you then put your pens on a layer above that and have the stroke information drive the animation path of the pen. It may look like stop-mo but isn't really.
If you don't want to draw it out, or are not an actual artist/calligrapher, you can derive strokes, I believe, from a pre-existing piece of line art in vector art file format (.ai )like from Adobe Illustrator, stands to reason AE should be able to take the data from the sister Adobe application and work with it... but this is speculation on my part, I'm not an AE guy. You should ask about this in the AE forum for actual implementation notes.
You can combine the 3-d CGI and 2-d compositing and get something really realistic if you wanted to. Pens and virtual camera in lightwave, the paper in AE, for example.
A real stop-mo program I like a lot is Boinx iStopmotion. It can do stop-mo as well as time laspe and includes chromakey, onion-skinning, looping, a lot of pro type tools. On the PC side, try anim8tor.