I am developing a web application that should display data points below the Earth's surface. It should also include user navigation, zoom, and rotational capabilities. It reads in the data from a XML file and should display 500-1000 spheres. Ideally, I would like to use HTML5, but it doesn't run in IE8. This is a Flash application that is somewhat similar to what I want (minus the globe around the spheres): http://demo.tufat.com/applets/molecule/index.html
There is also a good jQuery application that allows for 3d rotation out there.
So, the question is JavaScript/jQuery or AS3? I know Flash handles large amounts of data better but is Flash dying out? The application must run efficiently on most browsers.