If you know how to program in Java, I would create one in java and one in Flash, and compare the performance. I program in java as well, and know some of the benefits that are inherent to java, that do not exist with Flash. The animation will be better with Flash, but the usability and compactness of java will make it a better game across all browsers and platforms. Javascript isn't as powerful as java, so if you can program java, I would.
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