Answers should compare the best possible methods/libraries for drawing/animating the vector graphics on both platforms (particularly java, is there more than one way in flash?).
What are those methods?
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In Java I think your best method will be JavaFX, but you’ll find others on the links bellow. As it’s so new, there aren’t so many animation libraries etc available as there are with Flash.
Check out:
http://www.bubblemark.com/
http://www.craftymind.com/2008/04/11/why-bubblemark-is-a-poor-ui-benchmark/
http://www.craftymind.com/guimark/
for performance benchmarks.
In both tools you can create assets in SVG or Illustrator and import, or draw curves / shapes at runtime.
In Flex there is Degrafa now too http://www.degrafa.org/ – but the rendering engine is the same.