If these ideas have already been put out there, i apologize. These movies are old material, but i just had way higher expectations of these movies.
Episode I: Begin with focus on a young immature Obi-Wan, mirroring Luke, just before he meets Master Yoda. Let Yoda tell a bit of his origin, have him always like a cheerful hermit. While the Jedi are in their temple, Yoda would have found or made a swampy garden for himself to meditate, perhaps much like his home world (i am not lored on these things if they have already been established - this is just how *I* wanted the prequels to go), which would explain him seeming quite at home on Dagobah.
Have Ben meet Anakin half-way through the movie on a mission given by Yoda, but Yoda's not joining. Have them already about the same age, see each other as rivals, but some awesome mid-movie Star Wars event happens that joins them as friends and brothers.
Make Anakin's obsessive desire to better Obi-Wan in front of Yoda be the core of the conflict, but keep it light-hearted, it's only the first movie! But perhaps the climax event should involve a mysterious new Sith, Darth Maul. They all proceed to fight, but ONLY Qui-gon-Boring is killed.
(such a disgrace and an insult to the audience: in the FIRST movie after ALL that promo material featuring Darth Maul, and he plays no greater roll than BODY GUARD who DIES?!?!).
Episode II: Make it about the friendship and tension between Obi-Wan and Anakin. Perhaps Yoda could set up a mission where Obi-Wan is designated leader, or have Obi-Wan be declared Jedi before Anakin. Add further layers to his anger, impatience and vulnerability to dark suggestions.
Add Bail Organa in there somewhere here, as an eager to help friend, and ship-owner (hiding his identity as Alderaanian royalty for some reason)
Have them both meet Padme and fall in love, mirroring Han and Luke toward Leia, only without the incest. We all know who wins, but it would be cheeky fun to see them out-flirt each other, Anakin having more natural talent, and Obi-Wan being the jealous one this time. Add frustrated emotions that cause Obi-Wan to say things he normally wouldn't to hurt Anakin, further pushing him. Make these relationships at least realistic, GEORGE!!!!
Anakin starts listening to Palpatine, the "benign" support of a high politician with a sexy young senator at his side, wearing interesting, bun-like hairstyles all pulls Anakin further under Palpatine's dark wing. Maybe now Obi-Wan is declared Jedi after all this drama, and leads a mission where Anakin has to submit to Obi-Wan's decisions, their friction growing stronger.
Because throughout, have Padme and Anakin interract in cute, antagonistic ways, mirroring Leia and Han, eventually leading to an ending scene where Anakin and Padme escape together to a romantic location, and conceive twins...
Baby belly in Carbonite. Makes you care a little more about what happens next, even if we already know. But play it as if we don't! What really sucks is that there's no graceful way to save the surprise of Yoda's identity in Empire, AND include him in the prequels. But Ben said YODA trained him. Not some no-jedi with no personality named Qui-Gon-Fuckit.
At the end of the big fight, have Anakin burned and dismembered and rescued by the emperor. Have a "working" version of the suit put on him at first. The whole fun of seeing him get the suit should be in the evolution of the suit! Make him hungry for revenge against Obi-Wan. As he stumbles back to the bridge seething with rage through his electronic voicebox.
Meanwhile Obi-Wan, and Bail Organa separate with the twins on different ships, while Padme is delayed for some reason, but finally escapes whatever pre-destroyer they are in, all to meet at a rendezvous point. We'll have Padme insist they fly this way to ensure in the case of disaster, at least one child might survive.
Feeling his love snap into nothing, Anakin finally snaps into Darth Vader, and you see another evolution of the suit before the end credits, but still not quite the modern suit. Give us something to look forward to!