The main problem with the prequels is a lack of good secondary characters.
Primarily non-Jedi characters who we don't know what their fates will be.
For example, taking a few KOTOR1/2 characters and tossing them in:
Obi-Wan's old friend, Bao-Dur is a tech specialist for the Republic forces. He's the one who builds Anakin's mechanical arm, tags along to give firesupport in many of the battles and in the end is killed by Vader when trying to turn him back to the lightside. There's some exploration of his species and his attempts to keep from succumbing to revenge since his world was destroyed by the Sepratists.
Mira, a bounty hunter, was an old spacing companion of Anakin's (assuming that the prequels would start with him as a 20-30 year old character) who has a romantic interest in him. She has quite a grudge against Jango Fett, and often makes sarcastic remarks about how she's supposed to be the one who was cloned since she could do a better job. Pretty much a "man-izer" who holds her liquor and makes comments about how she'd like to strap stun-cuffs on any man she finds slightly attractive. She winds up dying when saving Obi-Wan from the clone betrayal, holding off a crack squad of Commandos.
Then the Jedi themselves needed some more characterization. Only Yoda and Mace seemed to have some dialog, there wasn't any sense of dynamics in the council.
Toss in Atris from KOTOR2, and then you have massive changes. The chronicler of the archives who has never had a padawan, screams about how Anakin is the doom of the council, is angered that she isn't allowed on the front lines, etc. A character people love to hate, and she jumps at the chance to kill Anakin when he enters the Jedi temple. She is defeated only because in her rage and anger she realizes that she's beating him through the darkside, stops for a moment, and then Anakin starts tossing her around the room, smashing her into pillars, with the force in retribution.
Dooku would have been a good villain, if he was in all three movies. Same with Greivous. Dooku and some of the lost Jedi could have led to some great scenes in Ep 1 and 2, especially if he honestly thought he was fighting the Sith but wound up dipping into the darkside to do it. In the end his attempts to defeat the Sith were what destroyed the Republic. Turn him into a tragic figure, the audience wants him to win and is frustrated at the inflexibility of the Jedi to join him against Plapatine who they believe will step down when the war ends. Have that the Jedi council believes that the Sith were annihilated and that the prophecy refers to Dooku since his actions are like those of a Sith, not realising that the True Sith lie in wait.
Anyway, secondary characters are where you add flavor in such a prequel. People that you don't know what will happen to them, so you can toss in some surprises and tragedy.
Similarly unexpected twists such as Anakin being a model Jedi, leaving the order for his romance (end of Episode I), and then taking on the force again to protect her (Episode II) from the sepratists and the only one willing to teach him is an exiled Jedi like Kreia from KOTOR2. Obi-Wan wants to teach him, but is forbidden by the council. Hell, ripping off KOTOR2 further, the Kreia type character might even be Palpatine's master and she's the one to hints to Anakin about Dooku not being his enemy but the True Sith hiding at the heart of the galaxy.
His using the force to protect a person, not the galaxy, leads him down the path that eventually has him making a pact with Palpy to save his wife.
