FusionCharts used Highcharts for rendering for a while, so in a way FC was a superset of HC. The two projects have parted ways last year, and FC has done great work through Raphael since then. I consider FusionCharts to be more feature rich, especially with some edge cases, but we chose Highcharts for three reasons -
1. SaaS pricing and licensing of Highcharts was more suitable given the scale of our team/application.
2. None of the unique features from FusionCharts had any purpose for our app.
3. At the time, Highcharts had better design out of the box (although FC has nearly caught up in this regard).
We have found Highcharts to small in size, quick in rendering, and flexible in structure to allow us add custom plugins, so we haven't looked back.
At this point I see the two options as very comparable on nearly every dimension, but it's still worth experimenting with both to see which one fits your style and product better (skinning, performance, flexibility for your feature-set etc).
1. SaaS pricing and licensing of Highcharts was more suitable given the scale of our team/application.
2. None of the unique features from FusionCharts had any purpose for our app.
3. At the time, Highcharts had better design out of the box (although FC has nearly caught up in this regard).
We have found Highcharts to small in size, quick in rendering, and flexible in structure to allow us add custom plugins, so we haven't looked back.
At this point I see the two options as very comparable on nearly every dimension, but it's still worth experimenting with both to see which one fits your style and product better (skinning, performance, flexibility for your feature-set etc).