Having just watched the prequels in the last week there were a few things I noticed that really stood out to me as to why they were so poorly received.
1) The plot felt scattered. Say what you want about the originals, but the plot was simple and always moving forward. The prequels spend a lot of time going sideways with subplots that don't really move things forward bu retread old ground that's already been explored.
2) Somewhat related to 1 - the connection between 1-2-3 just isn't there. New Hope, Empire, Jedi again kept it very simple. Yes time passed between those movies but what happened at the end of one directly influenced the stsrting point of the other. The prequels seem to start at random points because reasons. That makes the prequels feel like standalone movies with the same characters more than a trilogy.
3) Memorable moments. What genuinely memorable moments did the prequels have? I'm not talking scenes you might remember, but moments that get mentioned and are immediately met with a positive response? Darth Maul's lightsaber staff reveal, Anakin getting disfigured by Obi-Wan, Order 66. Does anything else really prompt a response?
4) Drawn out sequences. I'll just refer to the pod race sequence for this. Their was genuinely no way to move the plot forward without Anakin winning, they milked the "stacking the deck" moments way too much and then dragged the race out way too long. When the Rebels attacked the Death Star in New Hope it was always obvious they were going to destroy it, but the "how they get there" wasn't as poorly laid out as the pod race which made it enjoyable.
5) The music. Holy crap I didn't realise first time around how horrible the music is in important moments. This is a big part of why there weren't more memorable moments. Just take a look at Qui-Gon's death or Anakin losing his arm. Not only do they happen seemingly out of nowhere but it's almost like they caught the composer unprepared because the random lead up in both editing and music really takes the weight from the moment.
6) CGI. No I'm not talking about characters, lightsabers, blasters - just go and warch the Palpatine/Windu fight scene. Absolutely horrible CGI backgrounds. It's hard to get invested in the moment when every shot is a constant slap in the face reminding you how fake everything is.
I don't hate the prequels as much as most, but the combination of unfocused storytelling, poorly constructed key scenes and a lack of weight given to moments that should have drawn out emotion really do make the prequels inferior films. The individual elements just don't add up like they should have.