Empire is still my favorite of the six. If I had to pick a prequel, it'd be a toss up between TPM and RotS, because TPM has a plot that makes me go 'bwhuh?' but RotS ruins Padme as a character. AotC needs to be edited so that it's mostly Obi-Wan being sneaky, because that's the best of it anyway.

I have to say, there are at least two deleted scenes from TPM that I'm annoyed got cut. Anakin fighting with Greebo made perfect sense, especially with Qui-Gon finding them and giving Anakin the Look of Parental Disapproval. The scene where Anakin says goodbye to Jira is one where I'd keep at least the second half of it, because Qui-Gon destroying the tracking droid is cool, and makes Darth Maul's attack a tiny bit more suspenseful.