I'd make a completely different feeling trilogy by adding Count Dooku to Episode 1. I think if there would have been interaction between Qui-Gon and Dooku in Episode 1 and having them discuss "a change" that needed to be made because of the changing times and the Jedi becoming obselete or something it would have added to the whole underlying aspect of the Jedi being an old religion. It would have also made the characters of Qui-Gon and Dooku much deeper and it would make Episode 2 make more sense for people.
Example:
Episode 1-
When Qui-Gon learns of Anakin's potential he contacts Dooku on Coruscant, risking being discovered by sending a transmission outside the planet thereby tipping off Darth Maul, telling him he "might have found an answer" to their problems. That would add more tragedy to Anakin, making him nothing more than a servant to everyone, except Padme.
On Coruscant I would show a scene where Qui-Gon meets with Dooku to discuss their plans and they mention how they need to have Anakin trained so he could continue where they leave off since they are getting old. (They're trying to start a different Jedi order, Dooku has felt the presence of the Sith and feel the Jedi are helpless because of their "old ways"😉 When Qui-Gon is killed Dooku then decides a drastic measure is needed and we don't find out until Episode 2 that he has joined Darth Sidious but has become corrupted by getting too close. So at first when he's trying to convince Obi-Wan we feel he might be genuine in his thoughts, we later find out he has pretty much lost it.
Oh!!, and get rid of Jar Jar!!