I think on the graphing tool its as simple as the need to support IE6, 7, and 8. There are decent Canvas wrappers for relatively static content on IE (excanvas etc) and an increasingly interesting SVG wrapper at http://code.google.com/p/svgweb/ but for more dynamic graphics with sliding and zooming I've never found one that's good enough for production.

Has anyone had any issues with it? I think it is very robust and integrates so seamlessly one doesn't notice it's Flash unless you have Flash disabled. This is one of the 'appropriate and well implemented' Flash products. It's not broken in any way, so why fix it?