The one thing that I appreciated in the prequels didn't come until "Revenge of the Sith". It was when Anakin was crossing over. I appreciated that part of the story finally happening. I thought that was the best of the 3 movies. That was probably due to the fact that it was "darker" than the others.
I don't really dislike these movies as much as other people do. Do I love them? No. I don't hate them, though. I think that if you could completely forget that the original trilogy ever existed (let's just say they were never even made), the prequels would be, as far as movies are concerned, average, at best, for sci-fi/action. But the original trilogy does exist. So, when compared to those three films, the prequels are not good movies (barely even average). I don't mind most of the storyline to the prequels (there are a few things that I don't care for, too). The problem was the actual execution of the story. It is a shame, really. There was potentially something really good that could've been made and it was basically wasted.
Most of the major gripes I hear directed at the prequels feel too much like "nerd rage" - it's not like they were universally critically panned either, the critics gave them fair reviews. Here's just a few examples:
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Yoda using a lightsaber - um... he's a Jedi, so it's a given he's been trained to use a lightsaber
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None of the actors were as good as Harrison Ford - true, but it's unrealistic to expect every movie to have as great an actor as Ford. I mean none of the actors in the Marvel films are as good as RDJ, but that doesn't automatically mean the Captain America or the Hulk films are "bad"
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Jar Jar Binks - He was annoyiing and nowhere as entertaining as C3PO, but the series was already known to have "goofy" elements anyway - the R2D2 and C3PO antics, the Ewoks, etc
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C3PO being built by Anakin - C3PO was a generic type of robot shown in the films, so it's totally feasible that Anakin's slave owner purchased a "built your own robot kit" and assembled him from that - It's not like Anakin built him out of scrap metal or something
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R2D2 not using his jetpack in the sequel films even when it would have been useful in retrospect - maybe R2D2's jetpack had mechanical problems and had to be removed sometime between the prequels and the sequels - easy to explain away, just use some imagination.
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The Force being measurable in your bloodstream - It was already established that the Force was something genetically passed down, this is why Luke told Leia that she also has his power because she was his sister, and Vader was their father
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Kid Anakin winning the podrace and defeating the robot mothership in Phantom Menace - Just explain it away with "The Force" - it's not much different than Luke being able to destroy the Deathstar without his targeting computer after only a week or so of Force training
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Hayden Christiensen - I hear people gripe about him all the time, but I never hear a an actual reason given. My main gripe is that he turned to the Dark Side way too fast, and went from just wanting to protect Padme to wanting to overthrow the Emperor and rule the galaxy in the span of about 30 minutes. Other than that I have no complaints; if he's just "not as good as Mark Hamil" - well see the Harrison Ford post above.
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I didn't expect them to be as good as the originals anyway - I watched them for for the backstory, and how the Emperor rose to power and how Anakin turned to the Dark Side.