The prequels didn't contradict continuity. That is a lazy meme that has circulated by butthurt fanboys who can't accept that their precious head canon didn't come to pass, or that they honestly didn't know everything about the universe like they thought. The most commonly used example "how can Leia remember her mother if she died giving birth to her?" actually has a very simple explanation. The series has always strongly suggested that Leia's Force abilities are actually much more powerful than Luke's, and thus that she can remember far further back. Meaning that her eyes were open right after she was born, she saw Padme slipping away, looking "beautiful but sad", and it was burned into her memory. In fact, the novelization of
Revenge of the Sith explicitly states this, but Lucas clearly knew that it wouldn't look convincing if it was shot, much like the infamous baby shot in
Breaking Dawn Part 2. In addition, midi-chlorians are NOT the Force, but what allows individuals to be in tune with it (the more you have, the more aware of the Force you are); More resources to explain this below.
http://www.digitalspy.com/movies/star-wars/feature/a832013/star-wars-plot-holes-debunked/
https://www.retrozap.com/your-focus-determines-your-reality-debunking-star-wars-plot-holes/
http://boards.theforce.net/threads/debunking-plot-holes.20054360/
The prequels are not perfect by any means, but in truth, neither was the original trilogy. It too had moments of cringe-inducing dialogue, moments when the main character seemed whiny and unsympathetic (Luke and the power converters), and sidekicks that seemed overly annoying and pointless (C-3PO complaining to the point he seems to be rooting against our heroes, especially in
Empire) And these elements carried over into the Disney era. The rose-tinted glasses of nostalgia simply blind fans to it. But this is not me saying that the original films are bad, or that Disney's are. Simply put, they are all extremely good films that deserve to be credited and recognized as such. The only thing that would make the prequels objectively better was if Lucas had Lawrence Kasdan take a pass at the scripts and polish the dialogue. Everything else, from cast, characters, plots and visuals, couldn't be improved upon.
As for
Crystal Skull, it certainly is the weakest of the Indy films, but it not absolutely terrible. And again, nostalgia works its charm. We should rightly complain about the fridge, but we can't do it without giving the sledding scene from
Temple of Doom the same treatment. We also must remember that Lucas, while he certainly deserves credit for how it turned out, is not solely to blame, as much of the ideas also came from and were helped into shape by Jeff Nathanson, who was an uncredited co-writer on the script along with David Koepp, and went on to come up with the story of and writed the script for the most recent
Pirates of the Caribbean film.