The big problem I see with a project like Highcharts (and other Flot alternatives I've tried) is that features like animation and pretty aesthetics are center stage while performance is typically hugely lacking. We've driven Flot to its limit, and by far I can say that the winner of JS charting APIs is going to be the library that can perform well not just on Chrome but on Internet Explorer too.
We've charted things here that take under 1 second to render in Firefox/Chrome/Safari while taking 10-15 minutes with the CPU pegged (yes, you read that correctly) in IE.
We've gotten around it with a bit of work, but it's still a glaring problem for the APIs, and a glaring problem for projects that use HTML5 canvas, can't use excanvas.js with the Silverlight patch, but do need to serve up JS-powered charts to clients still on IE6/IE7.