My biggest problem with the prequel music is how "Duel of the Fates" was turned from a majestic battle theme into just another pour-it-on-like-ketchup song. When I first heard it on MTV's Total Request Live (the only orchestral song to make it onto TRL, IIRC), I was blown away by it, and by the images from TPM. By the time ROTS rolled around, it was like, "Oh, yeah, here's 'Fates' again, ho-hum."
That being said -- and to bring this on-topic -- I actually liked the fact that Adywan incorporated "Battle of the Heroes" into the Vader/Kenobi duel. It gives a sense of connection, with the same music as the backdrop for both their first and last duels. If it were me, I'd keep it in Revisited HD, but include an alternate audio track where the score is not used. Everybody wins.