One of the subtle things I liked in the PT was the inclusion of the Emperor's theme at the end of TPM. I liked how the tempo was sped up and children's voices added to replace the ominous male chorus... just different enough that I didn't recognize it at first, but upon second viewing, I thought to myself, "Cool... Palpatine is getting a foothold now, but no one realizes it." I thought it really justified the title "The Phantom Menace."