One thing I’d also like to throw out there: since Pencil has the capability of both vector AND raster, it would be great to integrate a program like Potrace into the mix. This is the same engine that Inkscape uses for tracing. I use it to trace BMP sequences into SVG, then I use InkscapeBatch (http://inkscapebatch.sourceforge.net/Homepage) to convert the SVGs to PNGs with alpha. If you just stick to tracing raster to vector, with maybe a specific layer devoted to “Trace”, you can scale the output of the animation to any resolution. The trace effect is also very nice and doesn’t require any anti-alazing.
I run Potrace command-line for the batch processing. Check it out here if you’re not already familiar with it: http://potrace.sourceforge.net/ It’s b/w only, but that makes it ideal for inking off a raster sketch. It also allows you to select the color of the trace and the color of the fill on the trace (if desired).