First, I would have loved to see the Darth Maul character explored more. Someone should of mentioned to Lucas to keep one ongoing villian throughout the trilogy, and not keep on introducing a new one every movie. In layman terms, it´s just plain sloppy storytelling.
Second, I like special effects, but CGI, to me, looks too real. When CGI is done well, especially with models, it looks okay (a good example of such is the LOTR´s trilogy). But, by itself, it looks too much like a video game.
For me, being a writer myself, I find the lack of any real story or character development in the PT disturbing... I know that most of the audience already knows the ending (i.e. Anakin being darth Vader, redemption from Luke, etc.). However, there could have been a few GOOD surprises thrown in there... Fondness for the characters lacked for me. I really did not like Anakin. I could care less about Mace Windu. Padme was blank. Even Yoda at times was about as wooden as Pinocchio. The only character I enjoyed watching on the screen for the PT was Ewan Mcgregor´s Obi Wan (and that´s a complement to his acting abilities, not the script itself).
Hell, one can find better plot, story, diologue and character development in the K.o.t.O.R. video games...