I'm glad to hear you still have to go through the edits one more time because I have a few more changes to suggest. Think this over:
As you'll see, I've thought a lot more about the end of this story. I now believe the final pieces of the Anakin story have to begin when he gets the message that Obi Wan needs to be rescued.
Following on the tails of the funeral scene-- Anakin's emotions about his mother need to be honored. It's the fact that Lucas drops all this material like a hot potato that completely unhinges the emotional story for the rest of this movie.
Our job (YOUR job) is to reconnect this wire.
Let's review: Anakin feels held back by the Jedi and Obi Wan in particular because he knows his mom needs him, but they won't let him go. He finally says "fuck it" and goes-- discovering he was right (GODDAMMIT!). Shmi dies and he has no one to blame... except Obi Wan. But right when his anger begins to surge -- the message comes: OBI WAN'S IN TROUBLE. What does our young Jedi Apprentice do?
Great question and a great opportunity for drama. Let's take it from there.
In broad strokes, I propose that Anakin goes to aid Obi Wan NOT because it's the right thing to do-- but (since he's mad about his mom) because he gets pushed into it. At first, Anakin is ambivalent enough to follow orders and let the other Jedi handle the rescue (which, we learn, would have worked out fine). He doesn't feel compelled to save Obi Wan until Padme decides it's her job. To avoid seeming "sickeningly PC" ;-)-- this has to be character driven. That means every cut that leads up to this decision has to support a clear point: that Anakin isn't sure what he wants to do, but Padme is.
Then, once he takes on Padme's challenge, he's there for the job and handles himself as best he can, but doesn't come around to be Obi Wan's friend again until their shouting match about saving Padme. Until the moment he agrees with Obi Wan, he's really only there for Padme and hasn't regained any respect for Obi Wan.
It's after he hears Obi Wan's compliments and Obi Wan's logic about what Padme would want that Anakin becomes, once again, a Jedi Apprentice.
How do I suggest telling this story? Well, I'm obviously revisiting stuff you've already done and I'm asking you to consider changing it. I believe there's only one way to address Anakin's feelings toward Obi Wan as the story requires and that's to show Anakin's mixed emotions when he first sees Obi Wan in danger on Geonosis.
We begin at the end of the funeral. Anakin speaks over Shmi's grave and R2 rolls up.
C3P0: "It seems he's carrying a message from..."
CUT TO: CU on Anakin staring down at his mother's grave, not interested in the droids.
C3P0: "...Obi Wan Kenobi. Master Anni..."
CUT TO: the droids as they finish their lines (skip the master of Anakin and Padme facing the droids).
C3P0: "...Does that name mean anything to you?"
Wipe to a master shot of the INT. SPACESHIP where Padme and Anni receive the message-- but only give us about two seconds of this shot for one word of dialogue:
OBI WAN: (on tape) "Anakin..."
CUT TO: CU of unhappy Anakin as the message continues to play. Then...
CUT TO: Master shot again until Padme turns... (cutting on motion)
CUT TO: CU of Anakin as Obi Wan instructs them to relay the message... (cutting on motion)
CUT TO: CU of Padme as she turns to the button. CU on button, etc.
That bit of doctoring keeps us keyed on how Anakin is processing this coincidence. He's mad at Obi Wan, but hearing from him now makes his emotions conflicted and burning. He's playing along as long as he's not forced to do anything yet...
The message from Obi Wan continues, intercut with Coruscant until Obi Wan's attacked:
EDIT: In showing this attack, reverse the close-ups of Padme and Anni. Start on Anni's reaction. He's surprised, but not moved... Cut to Padme, turning to Anni to see his reaction-- she's surprised by his reaction as well as by the message itself.
The message ends and Mace addresses Anakin:
Mace: "Your most important thing is [cut] to protect the Senator at all costs."
(losing the line "stay where you are.")
Anni's reaction is dour and unhappy. He's full of mixed emotion, but looks resigned to following orders. Truly, he's relieved to not be sent to save his master about whom he has mixed emotions for the moment. But...
Padme explains-- it's less than a parsec away. Are you really going to let your friend die?
CUT the line "He's like a father to me." Just have Anakin walk away from her plea. He replies "They gave me strict orders." He ain't budging-- he will follow orders, because he doesn't want to face the real issue: his anger at Obi Wan.
Padme ain't listening: "They ordered you to protect me, and I'm going, so you have to come." She stubbornly starts up the ship... Anakin watches... he does not stop her, but NEITHER does he smile (the sequence works as is up until you have to CUT the smile). He's in love and in awe of Padme. He won't stop her since her actions are noble. He's a sucker for noble actions-- even if he's not exactly in love with Obi Wan at the moment.
As a side note, I think this darker version of the scene makes the 3P0 lines at the end about "never having done space travel" more appropriate, so I hope you keep them.
NEXT STEP:
As Anakin and Padme fly into the plumes above Geonosis and we're watching the ship from the outside, we can have Anakin say some lines. These should introduce the subtext that's missing from these scenes which is "I'm doing this for you, Padme. Obi Wan is currently on my shit list."
I suggest a line like this:
EXT. FLYING SPACE SHIP OVER GEONOSIS
Anakin: (V.O.) "We have no idea where he is. If I'm to protect you, we need a plan."
INT. FLYING SPACESHIP
Padme: "See those columns of steam straight ahead?-- they're exhaust vents of some type."
Anakin: "That'll do."
That makes this little interaction a lot more interesting. Maybe you can come up with even better lines-- ones more loaded with "anti-kenobi" venom-- without being over the top.
They land. Padme instructs Anakin to follow her lead. "Don't worry," he says, "I've given up trying to argue with you." Now the resignation relates to something-- he's going to help her do something he wouldn't do without her encouragement. Your reading of the line should emphasize THIS point rather than the current reading which is sort of "tired old married couple" banter.
Then the great changes you've got take over-- the factory [OMIT the reference of "Obi Wan's going to kill me" when his light saber's destroyed], the kiss, the CUT TO int. Arena where we see the columns and Obi Wan tied up.
Here's a big moment: Obi Wan and Anakin see each other for the first time. Obi Wan's surprised-- Anakin DOES NOT SMILE at him. He glares. Obi Wan rolls eyes.
The couple are chained up and Obi Wan says "I wondered if you got my message." Anakin replies as scripted-- but the line reading is sinister and flat. "We got it. Then we came to save you, dick-head." "Good job" cracks Obi Wan. Do NOT show the embarrassed Anakin reaction shot.
The animals come out. CUT Anakin's "I got a bad feeling about this" line-- CUT the "what about Padme" lines. Anakin and Padme have a plan. They spring into action and Obi Wan is the one playing "catch up"-- not Anakin.
Relocate the center of anxiety in this scene to Obi Wan by using the following ideas:
Recut the action of the beasts so that Anakin's beast ATTACKS FIRST.
Then Padme's.
Then Obi Wan's. Obi Wan is left tied up the longest, the last to be attacked and the last to escape.
As the beast stabs at Obi Wan, pump up the anxiety with bigger BOOM Sound FX as the beast misses and crushes the ground.
Keep the tension building on OBI WAN and PADME as their struggles play out. Keep the Anakin "training the beast" beat for last. In other words, let the beats of Obi Wan and Padme play out AS MUCH AS POSSIBLE before Anakin gets anywhere with his attempt to train his beast. BUT...
Once things are terrible and Anakin approaches his beast with his hand outstretched-- play the FORCE MUSIC CUE. The force has a strong effect on the weak minded. Let's hear it -- and now we know Anakin's plan.
Then, in much more rapid cuts than the present edit, Anakin rescues Padme and Obi Wan. Let Anakin's success unravel their mess more quickly and directly.
Up in the stands, Nute Gunray complains. Dukoo reassures him and finally:
THE DROIDS roll out... MUSIC CUE: when these droids come we need much scarier music. This should sound like the end of the frickin' world!
It's all over...
Until...
Mace shows up and the next battle begins. etc.
(As a side note in this battle: PLEASE cut the beat where Padme and Anakin jump onto the chariot and run around. Natalie Portman looks so silly holding that gun. These beats advance the story not one bit and their "banter" about "aggressive negotiations" is terrible. Please omit this entire bit. It bothers me as much as the C3P0 stuff. Losing it will speed up and intensify this battle. Please.)
The last great Anakin beats come as he and Padme ride with Obi Wan on the gun boat. Anakin naturally takes charge: Shoot at the fuel, he says. Good idea, compliments Obi Wan. That's a nice change-- maybe Obi Wan's not so bad...
Then Padme drops out and Anni goes nuts. Obi Wan gets in his face and challenges Anakin to now or never act like a Jedi! Anakin accepts the challenge and lets Padme go. Maybe a special music cue is called for here, I don't know. But this is the key moment at the climax of this character story.
I hope these ideas are clear. Thanks, Trooperman. I love working on this.
As for the "suicidally stupid" attack on Dukoo-- I think the important thing to cover is that it at least seems like a good idea. If Obi Wan says "Don't rush him" and Anakin rushes him-- it's like comedy. So the quick fix is to not have Obi Wan say "Don't rush him." If it could be worked into an even better beat, say, Anakin shows some patience, then Dukoo baits him and Anakin finally sees a chance and attacks what he thinks is a weakness-- well that would be awesome. If it can look like Anakin's doing something great and decisive only to be stopped dead, shocking him and the audience as well-- that's the best possible version of that beat.