When the Star Wars prequel trilogy (ie. episodes 1 to 3) were announced, it caused an absolutely massive amount of hype because it had been 16 years since the last mainline Star Wars movie, and fans were absolutely excited. The theatrical release of the first movie in the trilogy broke world records in the amount of people lining up to movie theaters and, especially, in the amount of time they did so: Indeed, at many places people were camping in line for literally weeks in advance. (Lining up for the premiere of a hyped movie for an unreasonable amount of time was not unheard of, but this broke all previous records by a landslide.)
Then the first movie came out and... to say that it caused mixed feelings is understating it. For many fans the absolutely massive hype did carry on for quite a while and they were still excited about the movie for months to come... but even they started to experience a bit of doubt once the hype had passed and they could analyze the movie in a more level-headed manner, particularly after re-watching it a couple of times more.
Some fans were somewhat disappointed from the get-go, others became a bit disappointed in retrospect after the initial hype had passed, but most of them were still defending the movie and hoping and expecting that the next two movies in the trilogy would make up for the disappointment and be awesome. Sure, a few fans were still saying that the movie was a masterpiece, but they were in somewhat of a minority.
Then the second movie came out, a lot of people once again lined up for the premiere (although in somewhat lesser numbers and less time than for the first one) and the hype was really high once again, and after seeing the movie... once again mixed feelings. Some loved it, some were a bit disappointed, although most of them couldn't really put their finger on why exactly.
For most fans hope was still not lost: Surely the third movie, the "finale", would redeem the entire trilogy, and save it from disgrace? Yet, the exact same story repeated a third time: Long queues (but not as long as for the first movie), a lot of hype and excitement, lots of mixed feelings after seeing the movie.
The entire trilogy got a huge amount of backlash and criticism starting from the very first one, and even the most avid fans couldn't defend it very strongly. Some fans were still clinging to it and saying that it was a good trilogy and they liked it, but the general consensus, even among avid fans, was that it was "ok but a bit of a disappointment." Very mixed feelings. Among less-of-an-avid-fan viewers the general sentiment was a lot more negative, and many outright hated the entire trilogy, and particularly the first movie.
There is an enormous amount of criticism, even very rational and reasonable criticism, that can be given for the trilogy, but almost all of it can be summarized by one single thing: George Lucas is a bad writer.
That might sound like sacrilege, but that was indeed the crux of the problem. He wrote bad scripts for all three movies. He should have really left the scripts to better writers and concentrated only on producing and directing the trilogy. He could have delineated the stories, but the details should have been left to world-class scriptwriters.
Anyway, that's not the "main problem" I'm not referring to in the title of this post. Of course it stems from the bad writing, but from all the problems in the script (and the movies in general), what is the one that could be considered the most fundamental?
Well, what is the core idea of the prequel trilogy? What is it about?
The prequel trilogy is the origin story of Darth Vader. That's what.
This is not just speculation or reading between the lines: It's directly the official canon. And, rather obviously, it can be seen in the movies: The main running plot and idea is how Anakin Skywalker became a Jedi knight and then joined the Sith, becoming Darth Vader. We follow his story from childhood, when he was first discovered by the Jedi Order, all the way up to him becoming Darth Vader at the end.
And the main and most fundamental problem with the entire trilogy is: This background story and particularly his turn to the dark side and joining the Sith is extremely badly written.
For starters, the total running time of the entire trilogy is about 8 hours. I have not gone through the trouble of accurately counting how much of those 8 hours is dedicated to showing Anakin's slow transformation and reasoning for his turning, but I would estimate that, at the very most, about 15 minutes is dedicated to it.
That's astonishingly little time dedicated to the very core plot and idea of the trilogy.
And, indeed, when you watch the trilogy for the first time, even knowing that this is the core idea, his turning to the dark side and joining the Sith comes a bit out of the blue, without much explanation, without much reason. There's extremely little in the trilogy that explains what happened and why he did it, how his thinking changed and what lured him. There are a few scattered scenes here and there, but they are very short and not very telling, and most of them are very simplistic, even childish.
This is the main problem with Lucas' bad writing: He spent way, way too little time showing Anakin's psychological transformation, and even the little that he did show was badly written, making his turning feel like unjustified, unexplained and random. It almost feels like Lucas himself couldn't figure out why Anakin turned to the dark side, or couldn't figure out how to explain it, and he struggled to insert at least a few scenes trying to show something about it.