You are one ambitious dude. I love to read about your plans and the way you phrase your intentions. Makes me think it's gonna be great.
I suggested up-thread that Anakin should have a different sense of motivation when we meet him: Obi Wan should be holding him back from running off to save his mom. Here's my idea (sorry it's long):
The concept is to replace Anakin's brash, disobedient characterization with quiet and mysterious. I want to change the Anakin/Obi Wan relationship. Currently, Obi Wan is patient and forgiving of Anakin's head strong behavior. My suggestions make Obi Wan overly disciplining and Anakin obedient, but mysterious.
This fits Obi Wan's hesitation about Anakin in Episode I. If Obi Wan worries to Qui Gon that "the boy's dangerous, they can all sense it, why can't you?" Then why wouldn't he reign this brat in? He would. Maybe even a little too much.
So, here's my strategy (I'm using MagFan's Episode II as a starting point-- maybe the release version contains opportunities I'm not seeing, but MagFan's treatment gives this stuff a good boost, especially as regards Jar Jar):
We first see Anakin and Obi Wan in the elevator traveling up to Padme's. Obi Wan says Anakin seems nervous, Anakin says "Not at all" cut to: -- "You're sweating, relax. Take a deep breath..." Then CUT out of the scene before we know what's bothering Anakin.
They meet Padme and she finally notices Anakin. Padme: "Anni?" (cut the "My goodness you've grown")
Anakin steps forward with a new line (covered by cutting to Padme): "At your service... Senator."
Padme smiles and leads them to the seating area, saying she thinks this is unnecessary.
Typho explains the situation and Obi Wan says "We're here to protect you Senator, not
to start an investigation." -- CUT any quibbling with Anakin. Anakin watches and says nothing.
Create a pause to indicate the difference between what Padme is asking for and what Obi Wan is offering. Use their different gazes to indicate that there is something unsaid between these characters.
Padme finally finishes the conversation by replying: "Perhaps with merely your presence the mysteries surrounding this threat will be revealed. Now if you will excuse me, I will retire."
They separate and Anakin stops beside Jar Jar. CUT the line "She hardly even recognized me Jar Jar" and just let him silently watch Padme leave the room. Then he says the line "She's forgotten me completely." This makes him more mature and smart. It reveals all his emotions, but stops him from looking so out-of-control.
Then Obi Wan scolds him "Anakin, you're focusing on the negative again. Be mindful of your thoughts." And try to CUT out of the scene before saying "she was pleased to see us" if you can.
The next scene to adjust is Obi Wan and Anakin guarding Padme as she sleeps. Let it start as Obi Wan enters to find Anakin. He asks what's up and Anakin says "Quiet as a tomb." Cut his next line "I don't like just waiting...etc." Go straight to "She programmed Artoo to warn us if there's an intruder," and cut in to see Padme asleep. "I can sense everything going on in that room." Let this be the Jedi's plan as they rely on their senses to detect anything Artoo can't -- avoid the idea that Anakin has some unapproved plan to use Padme as bait -- it undermines Obi Wan.
When we come back to Anakin and Obi Wan, Anakin's on the terrace. "You look tired," says Obi Wan. Anakin: "I don't sleep well anymore." Obi Wan: "Because of your mother?" Anakin: "I don't know why I keep dreaming about her now. I haven't seen her since I was little." Obi Wan: "Dreams pass in time"
Then CUT as Anakin moves inside and Obi Wan continues: "Be mindful of your thoughts, Anakin, they betray you. You've made a commitment to the Jedi Order... a commitment not easily broken..."
As we CUT into Padme's chamber, Obi Wan continues berating Anakin using dialogue from their previously cut exchange in front of Padme. Obi Wan: "We will not go through this exercise again, Anakin. And you will pay attention to my lead... and you will learn your place, young one."
Cutting back to Anakin -- he senses the intruder in Padme's chamber -- Obi Wan does too and they leap into action.
What this does is establish the problem between Anakin and Obi Wan as stemming from his dreams about his mother. It says they've had to talk about it before and it's threatening the training. Later, when Anakin blames Obi Wan and the Jedi's for not trusting him, we'll know he's referring to this.
I would go through the rest of the movie and adjust Anakin and Obi Wan where ever possible to reduce Anakin's insubordination and increase Obi-Wan's hardness.
The last piece I want to complete this thread needs to be created. I don't know exactly how. It is this: We NEED to SEE Shmi in danger and KNOW it's from Anakin's dreams.
The pieces exist I believe of Anakin squirming in a bed, troubled by his dreams. Superimposing the first image we get of Shmi tied up over that for a few frames creates the bit we need. Then drop it into the story at the FIRST possible opportunity. The sooner the better because it informs everything Anakin does.
I hope I'm being clear and sounding sane. I just know this version of Anakin makes me root for him in the love story and everywhere else. It follows up the young Episode I Anakin better and sets up why he would turn away from the Jedi and toward a "secret" love. That's what was supposed to happen in this movie.
Good luck!