I think the biggest PT cock-up was Lucas not giving his basic outline to a professional writer or two to finish as three complete scripts before the first one started filming.
Lets face it Lucas has never been the best writer in the world. He isn't even that good a director. He is a good executive producer and ideas man but those ideas have to be managed by someone whom he respects. He doesn't understand why his 1977 film is so loved so having it written by someone who does get it should have been essential.
The OT was made up as it went along too but somehow largely got away with it until ROTJ. After ROTJ went off the rails story-wise Lucas should have used it as a learning experience on the importance of story and script. Instead he learned that he could shove anything in under a Star Wars crawl and no matter how awful it will always make money, which I suspect was Lucas' main goal. After ROTJ the general feeling was that Star Wars had become too much of a toy advert and too parasitic on itself. If anything the PT is everything wrong with ROTJ on a more hideous scale.
You know how Obama got the Nobel Peace Prize? It's probably the same reason people don't bitch about Jedi so much anymore. It's not George Bush.
The near contemporary LOTR and the Harry Potter films benefited greatly from being adaptations of pre-existing material. It gave the people behind those projects a sense of direction to move towards.
So much of the PT seems contradictory to itself let alone the original trilogy.
A respected professional writer would have found a way to make some of Lucas' more out there ideas work and had the balls push the button on the ejector seat on those that could never work.
Jar-Jar was clearly meant to be a major character in all three films but the racist undertones of his persona made him terminally unpopular.
Anakin was clearly meant to attempt to liberate the slaves in Episodes 2 or 3 (his prophetic dream was telecast in such a way that it must have been the original intent).
The mystery elements in Episode 2 were meant to evoke detective fiction but they didn't work and were not returned to.
The lack of a central villain or twist in the obvious observation that Palpatine is the puppet master left a blank space where the antagonist should have been and the protagonist should never have been an OT character as we know their arcs.
If Anakin and Obi-Wan were background characters we would have a protagonist we could really care about and feel genuine anxiety about because they are new and may survive beyond the OT. The fall of the Republic and rise of the Empire would still happen, Vader could betray the Jedi but the focus would be on someone unique to the PT.
Having Yoda in the PT was a mistake in my opinion and having him be a saber throwing acrobat was a disaster the series will be hard pushed to recover from.
Jake Lloyd was clearly cast to resemble a certain Titanic victim, he doesn't look much like Hayden but is the spitting image of Kate Winslet.
So the contracts should have been drawn up before the first film rolled. If the actor they wanted wasnt willing they should have cast a young Anakin that resembled a younger version of their final choice or maybe dropped the stupid Kid Vader idea in the first place.
Dooku would have been so much more tragic/potent a character if he was the same character Liam Neeson played in TPM leaving Obi-wan to do all the ground work of finding Anakin.
While there is nothing wrong with having clear touchstones evoking the OT, the FNWNK in the PT is fourth wall demolition. Threepio is now Princess Leia's older brother!!!!!!!!???? Boba Fett is the son of the bodyguard of the leader of one side of a war who also happens to be the clone template of the whole army on the other side !!!!!????? AND BOTH SIDES KNOW THIS AND DON"T SENSE SOMETHING A BIT IFFY AND BOTH SIDES USE THE FORCE!!
And yet we don't see Cyborg Vader kill Jedi *grrrrrr*
These things needed to be sorted out before TPM rolled (between 1983 and 1999). A proper professional writer would have taken that time, shuffled the plot ideas around for maximum impact, giving the production team direction and focus, someone to care about in the chaos and some surprises despite it being a prequel series.
Known directorial talent would have been an obvious plus too.
These films were anticipated for decades and will never be made again. Even if the ST is brilliant and there is no guarantee of that, the mistakes of the PT will always be the ghost at the party.