I'm sure novels could be written about what's wrong with the prequels, Mister Plinkett sums it up nicely. I'll just say that the three biggest missed opportunities were character development for Maul, Doku, and Windu.
Maul: Not a single spoken line. What was he fighting for? Did he have a slave family, wife and kids, who were promised freedom if he aided Palpatine? We never know.
Doku: He used to be a Jedi, and was said that murder was "not in his nature" for it. So basically a light-sided Sith Lord, a precursor to Darth Vader in a sense. What went on inside HIS head? Why was HE aiding Palpatine? We never know.
Windu: An emotional, anger-filled Jedi. A walking contradiction, who walks a very thin line. Could have been the single most badass character in the entire trilogy.
Well you should try the star wars books then, the character development is done pretty well in them and most of them are accepted as canon. For example Windu is never angry but is instead able to channel his inner bloodlust through his unique form of fighting style, he's not at all emotional either and is one of the most stringent observers of the Jedi code etc etc.
As for Dooku,he's kind of an aristocrat and a politician who is tired of the Jedi hippie bullshit and he is the apprentice of palpatine who is the true Sith lord. He's also not too worried about killing anyone but prefers to not get his hands dirty doing it.
As for Maul,he was taken as an apprentice of palpatine before Dooku and was basically raised to be a Sith assassin. Besides sith doesn't have family anyway,too hardcore for that stuff. As I said a lot of the background lore comes from the books,so try it if you're interested in the lore.