Its hard to tell what did the most damage to the whole prequel concept, the idea of Darth Vader as a troubled teenager, or Palpatine's brilliant plan that made absolutely no sense. The first caused at least me to stop believing that the Hayden Christiansen character really was Anakin Skywalker, the future Darth Vader, which was not good for my enjoyment of the prequels because they are singlemindly about how Anakin Skywalker became Vader. OTOH, the convoluted plot of the AOTC took one of the few things I quite liked in TPM, the idea of Sideous quietly manipulating everything from the shadows, and ruined it.