Drop Phantom Menace entirely.
It's pointless, has painfully bad ideas like Vader as a precocious tyke, the grand romance starting out as a weird thing between a near-toddler and a teenager (who are somehow the same age in the next film), and and of course, JarJar. The only good things in the film are dead-ends, like Qui-Gon and Maul, who end up not meaning much to the overall story.My thought was to merge AotC and Sith into one film, since IMO each has good scenes, but require editing with a hacksaw to make them watchable. Perhaps it would just be better to have Sith alone, at about 90 minutes, since I can easily see how people would find Sith alone much more satisfying than watching the entire PT. Neither AotC or TPM contain anything vital to the understanding of Sith, and instead create plotholes and redherrings that distract from (what should have been) the focus.
In toying with the idea, I cut Grievous entirely. He's a weak character created solely to sell toys. The early sequence on the ship works better w/o him (it places the emphasis on Dooku and Palpatine, where it should be, IMO). The difficulty it creates is that ObiWan disappears for the middle of the film if his (fairly dull) pursuit of Grievous is cut. I have some ideas to remedy that, which I may explore if I decide to revisit this idea. Currently, 3 weak prequels have sapped my interest in Star Wars for now. :/
I will say though, that a great deal of the problems in Sith can be easily fixed by simply cutting the fat: the bad lines, the pointless exposition, and the scenes that actually hurt the movie by existing ("she's lost the will to live - beep boop beep"). If Lucas had had a bit more patience in the editing room, he might have turned out a film that would have satisfied us all...