It's the way the force is established in the prequels that bothers me so much. It has been demystified to the point of DBZ style power levels, and the defining feature of Jedi seems to pretty much be their ninja abilities. With Obi Wan, you never knew what he was going to be capable of next, but it usually involved using the force to outwit the foe. Then when we saw that Yoda could move massive objects, it was a big surprise and showed how in tune with the force he was. I think the best allegory for the prequels is how they ripped off this concept to have him throw things at people.The SW novel also adds an interesting introduction which outlines the events leading up to the movie. It actually is pretty much the political story of Episodes I-III-the Fall of the Republic, the Clone Wars, the Jedi purge-with one major difference-the Emperor is portrayed as weak and a recluse (and no mention is made of him having the force), hardly the mastermind of the movies.
If the Emperor was so powerful, it was because he was malevolent. It's ironic that he said in Ep. III that the Sith and Jedi are almost exactly the same - and that's completely true! They all get all kinds of worldly power and it turns down into a struggle between rival factions. It would make more sense if he had no power but was still evil...and the way I always saw it was that he was reclusive because he was basically this completely evil guy who had to pull the strings from the shadows.
The prequel novels aren't really straight adaptations, they have a lot of added material that isn't in the films, such as the history of the Sith in TPM, a lot of stuff in AOTC's opening and Anakin's motivation makes more sense in the ROTS novel.
All the novels also pretty much use most of the deleted scenes, such as the Biggs stuff cut from the original film. I think the reason it was cut was to make the opening fast paced and not disjointed-originally the blockade runner scenes were mixed with the Bigg's scenes (Luke sees the space battle, for instance, while repairing a Moisture Vaporater).
There was an excellent 'making of' on Youtube for the original movies that showed these. I wish I could find it: it kept the pace of the films exactly, but overlaid them with a pre-production scene portion every now and then.