Paint.net is an incredibly useful tool, and I use it extensively. However, an incredibly useful feature to implement would be the ability to add layers that are vector based (a la inkscape).
This functionality would be incredibly useful for graphic design as well as annotations.
For example, putting editable text and arrows in a layer that could be moved as the raster items move would be very beneficial.
I'm not certain if the code base could easily incorporate something like this, but it would be a neat feature.