Recently I used both Adobe Flex 4 and Java Fx 1.3.1, I agree both are very powerful Rich internet graphic application development tools.
My take on Adobe Flex 4 is, it is very easy design tool. It take care of lot of programming part by automatically generating the code. So my vote is "Easy Tool". If you make any change to data source , change a label identifier etc, it generates code and corrects any reference inside the code.
Java Fx 1.3.1 is little more difficult as compared to Adobe Flex, but there is no comparison the look and feel, "Graphical Effects" and this best in terms of Java compatibility.
Adobe Flex 4 builder is not free
Java Fx 1.3.1 + NetBeans is free. This makes a lot of difference in freelance developer community.
Again this comparison not applicable for "Desktop application" vs "mobile application" vs "web application"
There are further limitations for both in terms of Printing, download application to excel or csv, etc..