I ve done a fair amount of work with Protovis and a few things with D3. In addition to the points you mention, I think the following differences stand out for me:

• Where Protovis provides a simplified abstraction layer between the visual properties you re specifying, D3 uses the actual CSS and DOM specs - so instead of .width(10) or .fillStyle( #00C ) you d use .style( width , 10) or .attr( fill , #00C ). In these examples, the difference is pretty trivial, but when you re doing something like drawing a line in an SVG image, there are big differences. The result is that using D3 can feel a little lower-level - you have more control, but you have to be pretty familiar with SVG syntax to do some of the things Protovis does much more easily.

• As you note, Protovis is all rendered in SVG, while D3 can use other parts of the DOM. This means that, for visualizations that don t require SVG-based visual elements, you can use D3 even with browsers that don t support SVG. It also means it s much easier to integrate HTML and SVG in the same visualization, which is really nice for things like dealing with text (text manipulation and layout is pretty weak in Protovis).

• D3 changes or drops some of the basic Protovis utilities like scales and data manipulation. I m repeatedly annoyed that basic utilities like pv.sum() or pv.mean() don t have D3 equivalents, though some, like .nest(), are shared across the two libraries. Edit 10/1/12: D3 has filled out its data utilities, but there are still a few that Protovis includes and D3 doesn t, e.g. pv.dict, pv.numerate, and pv.repeat. Presumably they were left out because they were considered less generally useful.

• D3 provides utilities for asynchronous requests. When I want this in Protovis, I generally have to use an external library (i.e. jQuery).

• D3 API documentation is almost completely lacking incomplete, compared to quite detailed docs for Protovis. Edit (8/30/13): D3 now has complete and detailed API documentation on GitHub, so this point is no longer relevant.

• Finally, I haven t done much with animation, but I think you re entirely correct - D3 provides more animation support than Protovis, especially in terms of animated transitions. Protovis can re-render some or all of the visualization on demand, but doesn t have any support for stepping through a limited-duration animation - you d have to code it all by hand with setInterval. D3 seems to make this a much more integral part of the library.

Edit (7/12/11): It looks like there s a new major difference - as of June 28, 2011, Protovis is no longer under active development, and the Protovis team is pushing D3.js instead. The last release is quite stable, so this shouldn t prevent you from using it, but it s definitely a point to consider.

There s a tutorial that covers the differences between D3 and Protovis in some detail. I agree with @nrabinowitz s description, though I will point out that we recently added extensive API documentation.

There is a recent paper from the Authors of Protovis/d3.js published 2011 http://vis.stanford.edu/files/2011-D3-InfoVis.pdf mainly about d3.js but containing some of the reasons why they changed certain things on the way from Protovis to d3.js.