Really broad strokes.
Episode One should have started with Obi-Wan already as the master and Anakin as his apprentice with some ending that shows where Anakin is heading and why. Have Palpatine clearly trying to undermine the Jedi with Darth Maul, who still dies at the end. It's mostly going to be Obi Wans story though. You can give it a somewhat happy ending to go with "yay the new trilogy is here". Maybe the news that Padme is having twins is that big happy ending, I dunno.
Episode Two should be where Palpatine is looking for a new apprentice, Obi Wan and Yoda are losing control of Anakin and he transitions into being Darth Vader with the suit and everything after getting into the fight with Obi Wan. All this should be some major part of the reason why Luke needs to be hidden away. I don't think it needs to be super "dark" here because you are going to go all in with "the bad guys win" in Episode 3 so maybe you have them saving Padme and the kids and have some scenes with her spending time with a very young Leia (to try and tie up that Leia does remember her ma in Episode Six).
Episode Three should have Palpatine and Vader in full on bad guys taking over the galaxy mode from the very start and be about Obi Wan and Yoda trying to get Padme and Leia to safety. With the solution being that Leia needs to be hidden away also. Could have easily been focused on getting the death star built but also with the plans being stolen (so maybe it could have 25% to 33% of the movie following a Rogue One esque story). So your big climactic scene is centered around a failed attempt to stop the Death Star from destroying some important location and killing some characters that have been well established over the previous movies (such as Padme).
Episode Three should have ended with Luke only a couple of years out from the events of A New Hope finding out that his mother is dead but his father is still alive or something like that, I dunno.
The prequels are not, in my opinion, as terrible as people make it seem. My younger brother was just a kid at the time Episode One came out and he absolutely LOVED it and it's sequels.
The problem seems to be that they DID appeal to their target audience but the question really is whether or not they should have been the target audience. You had people keeping this brand alive for 15 years spending money on even the briefest sniff of new SW content. Expanded Universe etc.
Fells like they just said "nah" to those people and made a movie for the kids. Fine.
From the perspective of an old Star Wars fan the movies are just a never ending series of small and not great decisions that all add up to a spectacular wasted opportunity.
Darth Vader is their most iconic and recognizable character and they hold off until the very end before putting him in the suit. Ridiculous.
Ewan McGregor is their MVP in terms of acting and he owns the Obi Wan character but they squander that for the entire first movie and a decent chunk of the other 2.
It doesn't help that the Matrix comes along in the same year as Ep 1 and courts the more grown up audience. Then Lord of the Rings and Harry Potter come onto the scene in 2001, between Ep 1 & Ep 2, and challenge the idea of Star Wars as the number one huge fantasy/action/adventure franchise.
Just a whole range of small disappointments and bad decisions that add up to the prequels being viewed poorly in retrospect.
Then of course the discussion around how bad the prequels are put MASSIVE pressure onto the people making The Force Awakens so they decided to play it super safe and people were fine with that because it did promise a decent new trilogy. Then Rian did his thing and that's that.
