Here's one central issue I have. Annakin Skywalker/Darth Vader.
In the original trilogy he has three phases. Mysterious and intimidating villain, dark secret and relation to protagonist, sympathetic and redeeming end.
Darth Vader was an amazing character, one of brilliant character design with the black samurai armor, the respirator and a voice (James Earl Jones) that made everyone pay attention. The depth that was revealed showed me someone I felt for, and imagined a tragic figure that fell from grace.
What I got was Annakin Skywalker, a whiny little brat who became evil because...because he was easily manipulated in obtaining his selfish goals? It is hard to take Vader seriously in the context established by the prequels.
Here, I'll have a go, and you know what, I'll keep Midichlorians too.
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We meet Annakin as a young man, a pilot who gets the attention of a jedi knight Obi-Wan because his "midichlorian count is high". Annakin is more street wise, managed to get out of slavery due to his wits and his powers (which he did not know he had).
Then we meet the jedis, they are NOT the protectors of truth and justice. They are bureaucrats, settling petty trade relations and border disputes. Over time they have become apathetic to the needs of the people and only seek to maintain their position and see Annakin as a tool.
Annakin is trained by Obi-Wan forming a friendship, but they conflict over issues. Annakin has a strong sense of right and wrong and thinks the Jedis should do more to ensure peace. Obi-Wan is the level headed one thinking politics have made such vigilantism obsolete. Annakin discovers his family (just mother or more, whatever) that he had left behind are still alive but is unable to save them due to regulations. He disobeys the council and frees them and the slaves, fighting the Hutts.
He is banished to Naboo on protection duty as punishment, here he falls in love with a queen and impregnates her. This causes a scandal and he is stripped of his knighthood. He grows bitter about the situation. Meanwhile the Emperor sends his sith (Maul?) to kill the queen. He does so, but not before she bears twin children. The Naboo claim a jedi (as sith would be secretive so mistaken identity) did the deed, they also cover up the two bastard children sending them far away from Naboo.
Annakin assumes the council has taken action to punish him. The Emperor steps in and offers him power to take vengeance and the ability to resurrect his beloved. So, he sends Maul tot est Annakin and Annakin goes crazy and kills his assassin (think Luke's rage when fighting Vader). He then goes to the Jedi academy and kills the younglings, on his way to the council. Obi-Wan is infuriated and confronts him. The battle is intense because of the weight of the characters and their relationship formed (I'd put this as climax of second film). Obi-Wan humiliates Annakin winning handily giving him the condition of needing to wear the armor.
The emperor uses Annakin's grief and frustration turning him into Vader who becomes more powerful thanks to the darkside and brings down the jedi council and gives rise to the empire.
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There, a quick bare bones story of Annakin, just his story in this universe, so no details of the empire and all in this brief tale. This Annakin would easily be more sympathetic to the whiner we got. Someone strong, righteous, stubborn and loyal who saw the hypocrisy of an order created on the basis of blood instead of the works and yet used their gifts to serve a republic that did nothing for the suffering of him and his people. He descend into madness as he needs power to accomplish his goals, but is perverted by his indignation into committing atrocities losing sight of the galaxy he originally envisioned.
