PALPATINE: "Oh, but I do [your majesty].
ANAKIN: So have you...grown more beautiful I mean [cut]...for a Senator I mean[cut].
TYPHO: I'm very grateful you're here, Master Kenobi. I'm Captain Typho, head of Her Majesty's security service. [cut]Queen Jamillia has informed you of your
assignment.[cut] The situation is more dangerous than the [Queen] will admit.
OBI-WAN: We're here to protect you [cut]Senator[cut], not to start an investigation
[cut]OBI-WAN: Do you know who it was you were trying to kill?
ZAM WESSEL: The Senator from Naboo.[cut]
OBI-WAN: Who hired you?
ZAM WESSEL: It was just a job.
YODA: Track down this bounty hunter, you must, Obi-Wan.
MACE WINDU: Most importantly, find out who he's working for.
OBI-WAN: What about [Queen] Amidala? She will still need protecting.
YODA: Handle that, your Padawan will.
MACE WINDU: Anakin, escort [the Queen] back to her home planet of Naboo. She'll be safer there. And don't use registered transport. Travel as refugees.
ANAKIN: As the leader of the opposition, it will be very difficult to get [her] to leave the Capital.
YODA: Until caught this killer is, our judgement she must respect.
[cut]MACE WINDU: Anakin, go to the Senate and ask Chancellor Palpatine to speak with her.[cut]
[cut] PALPATINE: I will talk to her. Senator Amidala will not refuse an executive order. I know her well enough to assure you of that.
ANAKIN: Thank you, your Excellency.[cut]
The entire apartment scene with Jar-Jar will be cut, as it will be implied he is the permanent Senator from Naboo (see later).
Btw, I don't know why everyone takes out "Don't worry, we have Artoo with us" I like the line; it's a natural thing to say in an awkward situation, and wouldn't be questioned if it was in the OT.
The entire scene of them walking the streets of Naboo will be cut. After the establishing shot of them landing in Theed cut to them approaching Theed.
MACE WINDU: Do you think these cloners are involved in the plot to assassinate [Queen Amidala]?
The alien dialogue is easy to change in subtitles.
MACE WINDU: Anakin, We will deal with Count Dooku. The most important thing for you is to stay where you are. Protect [Amidala] at all costs. That is your first
priority.
MAS AMEDDA: This is a crisis! The Senate must vote the Chancellor emergency powers! He could then approve the use of the clones.
PALPATINE: But what Senator would have the courage to propose such a radical amendment?
[cut]MAS AMEDDA: If only Senator Amidala were here.[cut]
Shot of Jar-Jar deep in thought; he is Senator of Naboo.
OBI-WAN: On his way to Naboo. He is escorting [Queen Amidala] home. I have to admit, without the clones, it would not have been a victory.
That's a pretty good overview of how to keep Amidala a Queen throughout. I have no idea the logistics of making that work technically, though. Thoughts?