To start off I will ignore bad dialogue and/or acting. No; for me, after 17 years (!!) Since the last prequel came out, the biggest problem was that it told the wrong story.
It should have been about a young Jedi Master called Obiwan Kenobi and how his renegade, unsanctioned, training of Anakin Skywalker ( a gifted pilot and incredibly strong in The Force, but mentally unstable) lead to the downfall of The Republic.
Despite my issues with TPM, there is the beginning of this idea at the end of the film - but it is never continued into the following films.
I wonder how I feel about this with qui gon existing if qui gon didn’t exist I wonder because if qui gon trained anakin he’d never turn into Vader because qui gon was the renegade Jedi the true Jedi. obi wan was in between all that so that’s why anakin turned but if obi wan and yoda were the only characters then the story would be vastly different.