Nearly every key element he had developed for a backstory during the course of making the OT, is painfully underutilized:
Episode I was the most damaging chapter to the entire prequel story, dozens of key elements are changed, or explained in a unoriginal and even unsatisfactory ways, Such as:
Anakin in Episode I, is portrayed as a nine or ten year old boy, which immediately places the core of Anakin's development on the shoulders on Episodes two and three, not only that, but another key character is left underdevolped, Obi-Wan... for 98% of the film Kenobi is left in the role of sidekick to a created charater (Qui-Gon), and this created character takes away the discovery of Anakin from Obi-Wan, takes away any development in relationship between Obi-Wan and Anakin...and tries to make an unplausible beginning of a romance between a 9 year old slave child, and a 14? year old Queen...
Midichlorians and immaculate conception...cop out plot devices, used as excuses for the Jedi to consider training Anakin, instead of actually having Anakin prove his abilities onscreen during the course of the Clone Wars or course of adventures between Kenobi or Anakin....making Anakin a 9 year old child makes Anakin fighting in battle and proving his abilities not very feasible...Lucas instead chooses to have Anakin prove his abilities in a Pod-Race and by "accidently" blowing up a droid command station....ooops!, as Anakin would say.
Episode two is handled a little better in the sense that some key plot points are used, unfortunately they aren't used well, and because of the failings of Episode I, only at the end do the Clone Wars begin. Instead of the Clone Wars being used as the backdrop for Episodes I and/or II for character development, the idea is thrown aside, Instead, Anakin and Obi-Wan are seperated for the entire middle of the movie because of a single Bounty hunter. Anakin is left not this time as a yipping 9 year old, but as a whiny adolecent sporting poorly scripted angst driven "I've got to have you" pick up lines..Obi-Wan is given a quest to discover the bounty hunter's identity, and in the process discovers a huge clone army being made from Boba Fett's father...financed by somone named Sifo Dyas, who we have to assume is either Sidious or Dooku.....again a waste, the bulk of the Clone Wars are explained off between Episodes II and III, poor dialogue ruins the relationship and development of Anakin and Padme', hardly anything is is shown between Palpatine and Anakin, or Kenobi and Anakin for that matter,except for some quibbles they have at the beginning and end of the movie....and for added measure Yoda is thrown in with as a cheap entertainment device with the suddenly uncharacteristic ability to flip around at hyper speeds with a lightsaber.
Considering the amount of ground that had to be covered ROTS was bound to be unbelievable and rushed...as was Anakin's remakably fast transformation to the darkside, the how quickly the Jedi were defeted by troopers...amazing considering the Ewoks managed to do it with relative ease, and the overnight transformation of the Republic to the Empire complete with Star Destroyers overlooking and Death Star in construction....Episode III is suprising considering a significant amount of time is again wasted on a loose plot point (Grievous) and the fact all the information left out of the other two movies had to be compacted into one movie, complete with filling loose plot points (which was unsatisfactory)......vaguely, this is why Lucas failed.