A few suggestions
I would slightly revise your opening crawl:
“After a thousand generations of peace and justice under the protection of the Jedi Order, the Republic is in decay. A menace lurks in the shadows of the galaxy, plotting a reign of terror.
“Meanwhile, the greedy TRADE FEDERATION has engulfed the defenseless planet of Naboo with a blockade of deadly battleships, preparing to invade, enslave, and plunder.
With the newly crowned Queen desperate for help, the Supreme Chancellor has secretly sent two Jedi to settle the conflict…”
Cut all of Obi-Wan and Qui-Gon’s conversation after “It’s not about the Mission, Master. It’s something elsewhere…elusive.”
It is illogical for battle droids to open a door to a room filled with gas. To solve this, restructure the opening action sequence:
The Trade Federation destroys the Republic Cruiser.
The Jedi leap to their feet and ignite their lightsabers.
Gas seeps into the vents.
Qui-Gon cuts into the door with his lightsaber, and the door disintegrates on the other side.
Battle droids approach the door.
Two lightsabers ignite in fog.
The Jedi destroy a few droids.
Then they go up into the ventilation shaft.
Cut the line “We’ve got to warn the Naboo and contact Chancellors Valorum.” It is impossible to warn of an invading army while accompanying an invading army.
Cut the flat “the negotiations were short” joke.
Cut Queen Amidala’s hologram speaking with Nute and Rune because the next scene delivers the same exposition.
Cut the reference to the “battle-hardened” droid army.
Cut “More did you spake?”
Cut “Yousa guys bombas.”
Cut “Coruscant, uh, wait, uh, that doesn’t compute.”
Cut Jar Jar summarizing the plot of the movie to Padmé.
Change the subtitles when Watto and Anakin speak Huttese:
“I was cleaning the bin.”
“Watch the store. I’ve got a deal to make.”
Revise this to:
“I was fixing the moisture vaporator.”
“It better be fixed, or else I’ll vaporize you.”
This introduces Anakin’s mechanical skills, characterizes Watto as a cruel slave master, and foreshadows Luke’s fate as a moisture farmer.
Cut “Are you an angel?” and open with Anakin bragging, “I’m a pilot, you know.” That sounds more natural and less cliche.
Cut Padmé’s “I can’t believe there is still slavery in the galaxy. The Republic’s anti-slavery laws . . .” She knows her people are in death camps; slavery would not surprise her.
You cut Palpatine’s reference to creating life in Episode III, so you might as well cut the line “There was no father. I carried him, I gave birth, I raised him. I cannot explain what happened.” In your edits, this is a setup without a payoff.
Restore Anakin shouting out “It’s working! It’s working!” above the pod engine. It is a rare moment of emotion.
Cut “Space is cold.” It sure is, but there is heat on spaceships.
Cut “The entire planet is one big city.”
Once Qui-Gon says, “I must speak to the Jedi Council immediately. The situation has become much more complicated,” cut to the Jedi Temple establishing shot. It is unnecessary for Palpatine to blatantly manipulate Padmé to propose a vote of no confidence; he subtly manipulates Padmé in the Senate scene later. Arguably, Palpatine’s reliance on blatant manipulation weakens his character, which would be stronger if he could manipulate Padmé into proposing the vote without directly suggesting it.
Cut Mace Windu’s line “We will discover the identity of your attacker.” This contradicts his later order: “Go with the Queen to Naboo and discover the identity of this dark warrior.”
But restore Mace Windu’s line “This may be the clue we need to unravel the mystery of the Sith” which is related to his earlier promise: “We will use all our resources to unravel this mystery.”
Cut Anakin looking for Padmé so he can say good-bye. Gifting her the necklace was a more emotional farewell.
Cut “Without the Viceroy, they will be lost and confused” because it would be more accurate to say “Without the droid control ship, they will be lost and confused.”
Padmé should still mention the droid control ship in her plan because the whole military strategy revolves around it. I would recommend recutting the scene like so:
PADMÉ: We can enter the city using the secret passage on the waterfall side. Then we can enter the palace and capture the Viceroy.
QUI-GON: The Viceroy will be well-guarded.
PADMÉ: We have a plan which should immobilize the droid army. We will send what pilots we have to knock out the droid control ship orbiting the planet.”
This clarifies that capturing the Viceroy is the goal, but destroying the droid control ship is the requirement necessary to achieve that goal.