Other than the bad direction and acting, which I agree, there really are no contradictions.
Yoda trained Obi-Wan in the use of the force first and Qui-Gon trained him in the field afterwards. TPM hints that Yoda had taught Obi-Wan at the very beginning of the film and AOTC shows that Yoda trains Jedi Padawans when they're young. Why is that hard to figure out?
The dark side isn't stronger, because if it was, Anakin would have defeated Obi-Wan, too. Plus, the Prequels never said that it was anyway, so I don't know how you came up with that.
Leia remembers her mother because she, being born after Luke, somehow had some mental connection with her mother while she was dying, hence the images and feelings that she retained in later years. The Force is strong with Anakin's children, right? It isn't real anyway, so why let it bother you.
Besides some of the bad acting and poor direction, there is still a lot of good things in the Prequels. A good edit could salvage these films. But if you're going to butcher the films to make it completely different and hopefully better, then you're looking at the impossible. So why bother? You're better off just cutting out what isn't needed and adjusting around scenes to make it more watchable and entertaining like what some fan editors have managed to do.