After setting up Anakin in the opening scenes here are suggestions for maintaining the cooler, more mature Anakin:
Speeder chase:
Cut most of the banter. Let the excitement of the chase take over without the bickering. Maybe keep "What took you so long" but omit the response. The next conversation should be when Obi Wan says "Well, you lost him." Keep their exchange up through the line "I hate when he does that." That gives them some history and makes Anakin good since he kept his mouth shut before pulling this cool stunt.
When he crashes Zam's ship and has to roll on the ground, cut the action so he recovers almost instantaneously and starts running after Zam -- make him seem unstoppable rather than having that beat where he holds his ribs and catches his breath unconvincingly.
I think all the ObiWan/Anakin dialogue through this cantina scene is fine until Zam is dying in their arms. Anakin's angry "Tell us NOW" should be cut, leaving only his first, more sedate line reading.
Padme packing to leave:
OMIT this entire scene (please!).
REPLACE it with the shots of Anakin asleep in a bed having a nightmare about his mother. This is the perfect place to reinforce Anakin's primary problem: his dreams.
Arriving at Naboo:
Most of the Naboo stuff should favor the deleted scenes over what's there. I recommend a different order to the deleted scenes. First, of course, they fly in and Anakin tells Padme as they walk that he misses his mom (good stuff) and that he's glad Padme is a senator. OMIT the meeting with Queen Jamillia as unnecessary, unromantic and slow. Then they arrive at Padme's house and see her sister's kids. THEN GO TO PADME'S BEDROOM -- play out the scene where Anakin sees Padme's pictures and her past BEFORE the dinner scene where we meet Padme's family. This has the effect of making Padme and Anakin more mature -- able to settle themselves like adults before rushing in to say "Hi mom!" It also fuels the subtext of the dinner scene and the following KITCHEN scene as Padme has already revealed her personal side to Anakin without being urged by her family.
OMIT the balcony kiss scene. OMIT the grassy picnic scene.
Play out the fruit-dinner-for-two scene, but omit the reference to Obi Wan being "grumpy" if he saw this. That makes Anakin seem silly.
HEAVILY RE-EDIT the fireside-chat scene. As it begins Anakin and Padme are sitting quietly in this intimate setting with things to say, but neither of them brave enough to say it. Anakin breaks the quiet with a single sentence: "From the moment I met you, all those years ago, a day hasn't gone by when I haven't thought of you." Padme does not reply. She looks at him. He looks at her. She looks at him. We move in closer from shot to shot. Finally she comes to her senses and says "I can't, we can't. It's just not possible..." and she stands (action covered by edits). Anakin says nothing, but watches her as she turns to him again. Then he stands and has another idea, "You know, [edit] we could keep it a secret." Padme says "Then we'd be living a lie - one we couldn't keep up
even if we wanted to. I couldn't do that. Could you? Could you live like that?" Silence for a moment. ANAKIN: "No. You're right." Cut out on one of the best line-readings Christensen gives in the movie.
Finally, on Naboo, the last scene to tinker with is Anakin deciding to leave. First, as the sunset begins the scene, we should be hearing a woman SCREAM and Tuskan Raider GRUNTS, Shmi saying "Anni!" and some man yelling "ANAKIN!" (That last bit from the voices that Yoda hears as Anakin kills the sand people later). This montage of sound should play until Padme comes out onto the porch with Anakin. Her voice should almost seem to make the yelling stop -- mirroring what Anakin says: "your presence calms me." Then, use editing to extend the last Padme beat -- let things soak in for her a little longer (using the close ups) before she says "I'll go with you." Then cut out before Anakin says anything else.
NOTE: that montage of sounds from Anakin's nightmare could be laid over Anakin one more time earlier in the film. I think it might be possible to take some shots of him at the window in the omitted "Padme's bedroom" scene and present them as if Anakin were at the window hearing Shmi's screams. This might be dropped in between scenes somewhere. Just to amp up the pressure - if it seems desirable.
Arriving on Tatooine
The shots of Padme and Anakin traveling together by cart are awkward and unnecessary. Cut from the master of the ship landing to a one-shot of Wato as Anakin says his first line to the pathetic little creature. Then cut to the master with Anakin, Padme and Wato and play out the scene. A Jedi finds his man immediately -- we don't need to see the "shoe leather" of how he got there.
Shmi dies
Cut the lines when Anakin tells the dying Shmi, "Stay with me mom, everything's going to be fine" -- just let him hold her helplessly as she dies saying "I love..." and lays her head back. OMIT the wide shot where he closes her eyes and stay with the close ups -- first Anni, then repeat one of Shmi dead, then Anni's final glaring flash of anger before cutting outside. This reduces the awkwardness of this scene greatly.
Shmi funeral
OMIT the awful eulogy. Bring up the music. After the sweeping master shot, cut to Anakin falling to his knees (omit his stepping forward). Then cut away to Padme before he reaches down awkwardly for a handful of dirt. Then come back to him for the lines "I promise I won't fail you again... I miss you so much." After adjusting the preceding Padme/Anakin scene (discussed upthread), this promise made over Shmi's grave will finally work -- meaning that he's trying to vow not to be a bad Jedi anymore. He's telling his mom what he wouldn't tell Padme -- he regrets killing all those sandpeople.
Obi-Wan's message
As Obi-Wan's message finishes on Padme's ship and in the Jedi council, OMIT the Windu line "stay where you are," so Anakin and Padme do not disobey a direct order. As Obi-Wan's message ends, we see Padme watching, she looks to Anakin... CUT TO: Yoda's lines, then Mace Windu's lines, then CUT TO: Anakin's close up reaction. Avoid the master shot where Anakin looks too laid back. Then let Padme talk about how close Geonosis is, let Anakin say "if he's still alive..." and CUT TO Padme saying "I'm going to save Obi Wan. If you plan to protect me, you'll have to come along." Intercut the Anakin close-ups where he looks upset to break up her flight-prep action and cut it so his reaction changes from upset to smiling. Then he sits down to fly away...
Jengo captures Anakin
Your ideas for the droid factory sound awesome. As that scene ends, I recommend using part of the Dukoo/Padme meeting scene or, at the very least, the trial scene before Padme and Anakin find themselves shackled together in that cart for the...
Padme/Anakin kiss scene
HEAVILY RE-EDIT this scene and it will work beautifully. First, the music is badly mis-cued in the original edit and secondly the dialogue is horrible. But the scene and the performances are good -- so try this: They stand together and Anakin reaches out to say "Don't be afraid." Padme replies "I'm not afraid to die." He looks at her. She looks at him with love. He looks at her with confusion, she looks at him with a little tear... closer we move until she says "I love you." He gives her a disbelieving look, but she looks at him with tears in her eyes -- we know she means it (this may require dropping out the dialogue on some shots and cutting so her lip-movement doesn't look like talking). Finally, they move in together to kiss and as they kiss the MUSIC CRESCENDOS! The current edit crescendos after they draw into the arena -- but by that time the important stuff is already over. This will work, the performances are there -- just held back by all that awful talking.
Finally, the battle scene where Amidala falls out of the ship and Obi-Wan has to fight Anakin's urge to stop and save her should stay -- that's great stuff and will work as-is to support this new Anakin story. I recommend keeping it as written.
BUT
The moment Anakin rushes in to attack Dukoo as Obi-Wan says "let's work together" comes out of no where. Even more so with these new edits. Try to cut it so that Dukoo zaps Anakin before Obi Wan and Anakin can get their plan together. That makes Dukoo more dangerous and keeps Anakin likable and smart. When he rushes in and gets whipped, he looks comically immature. It's beating a dead horse -- we get it, he has much to learn -- why does he have to look like such an idiot? Please consider this last opportunity to keep Anakin smart while still not a master yet.
With these changes, this movie will have a strong and likable Anakin. This will make him the Jedi who clearly has deep troubles and real love which in Episode III cause him to throw everything away for the chance to save Padme.
Good luck, Trooperman. I'm eager for you to knock this out of the park.