Will Duel of the Fates be in Episodes II or III?

While it would be nice, I don't think that it will. It served its purpose as the "theme song" of TPM and doesn't need to be repeated. On the other hand, other themes were repeated throughout the entire Classic Trilogy. DotF could be for the Prequels what the Force theme was for the CT. Still, I think DotF was engineered specifically for the Maul-Jinn-Kenobi fight so any other occurrances would be weird.