I'd like to know that too ;)
It seems to me a bit that the D3 is a bit more general approach (is it?) so more coding is needed than with the toolkit chart control - but the possibilities are greater....
Well I want to use a chart control and I'm not quite sure which to use... maybe the toolkit chart control because I expect that there will be more development and documentation with that...
But maybe there is somebody who really knows this stuff and is not just guessing ;)