1) No kid Anakin. Introduce him and start the prequels with Anakin being a teenage padawan. Introduce Padme as a Senator and use the Queen of Naboo shit as backstory.
2) One villain for all three movies, preferably Darth Maul. The prequel trilogy handled its villains terribly and since Maul, Grevious, and Dooku all die in sub-movie length time it detracts from the rise of Vader and makes Vader simply feel like the Emperor's new flavor of the month.
3) No Anakin being Force Jesus storyline
4) Flesh out Obi-Wan and Anakins relationship. Make them actually seem like believable friends. The Clone Wars TV show really helped with this.
5) No Yoda lightsaber fighting
6) No Emperor lightsaber fighting
7) Make Anakin's descent to the Dark Side more believable. The prequels actually started down a believable path in Attack of the Clones when Anakin watches her mom die and then goes ham on the Sand People (which is the best scene in the movie). But then they back off that and instead have Anakin get tricked into going Dark Side. Simply have Anakin get a taste for the Dark Side, like it, and not back down from that.
8) Have Anakin turn to the Dark Side relatively early in Episode 3 and turn into proper suit Darth Vader earlier in the movie. Make the final act of the movie Vader hunting down and murdering Jedi. Make the entire fall of the Jedi Order much scarier, tragic, and impactful.
9) Switch it up so Padme is the one lusting for Anakin instead of Anakin lusting for Padme. It makes more sense that Padme would be the one to coerce Anakin into breaking the Jedi no-love rule instead of the stupid "I'm a senator!" bullshit.
10) Palpatine's "evil" look is simply caused by prolonged use of the Dark Side, not because he took Force Lightning to the face.
11) Nobody besides Palpatine gets to use Force Lightning.
12) Less over choreographed fights. The lightsaber fights in Episodes 2 and 3 are fucking awful when it comes to having tons of unnecessary flips and twirly bullshit. The Maul fight in Episode 1 is actually better about this and feels like a more believable fight between trained lightsaber users (based off of what he saw in the OT).
13) No C-3PO and R2D2. They're pretty unnecessary for the prequels.
14) No Padme dying of a broken heart.
15) More practical effects, less CG
16) Do all of the Stormtroopers really need to beBobaJango Fett clones? Like the "Anakin Force Jesus" thing, this felt like the franchise being too self aware of one character's popularity.
17) More dynamic camera work, less soap opera cam-1 cam-2 type stuff.
18) Less Jedi being killed by people who aren't Darth Maul or Darth Vader. The Geonosis battle pretty much murders the mystique of the Jedi because it shatters their aura of invincibility. Keep the Jedi deaths reduced, this helps make Vader's rise more impactful once he starts offing Jedi.
10 his face is messed up as a side effects of using force lightening.
He's the best who ever used it