I really can't pick a favorite, I like them both very much. I mean, PM you have a great introduction, an nice expanded explanation of the Force, how do you connect to it? How did the old Jedi get apprentices? They invented the best word Padawan, everyone SW fans says it and you know it. So many awesome characters introduced and the story arcs of Obi and Anakin begin. With Clones you really get into the Clone Wars, why Yoda said of Anakin, "Powerful Jedi was he", great stuff with Obi-Wan, a nice explanation with Shmi, the Lars, and Anakin's first true fall to the darkside. Round that out with Qui-Gon's voice, Jango Fett and Boba Fett's introduction (awesome), Count Dooku and the curved blade (equally awesome to Maul's double blade), I honestly can't make up my mind. I'll just say they're both great, completely worthy of the Star Wars name and I never watch the Classic Trilogy (OT or SE so far) with watching TPM and AOTC first.

And that's my two cents on the issue.