Yeah, it's a good idea, but difficult to work out. It also matches with what Lucas had originally planned for Qui-Gon in one of the first drafts of TPM: Qui-Gon doesn't show up until Obi-Wan arrives at Coruscant with the Queen, and accompanies him to Naboo where he is killed by Maul.

Qui-Gon kind of is the main character in this movie I suppose (though I think TPM is more of an 'ensemble' movie). Take him out, and the other characters can't make up for his absence. Still, would be very interesting to see how the movie would turn out without him. Maybe it's another option to make Obi-Wan a junior Jedi knight? Remove all references to him being a Padawan, and make him more of an equal to Qui-Gon. Maybe the mission to Naboo is his first as a Jedi, just like Anakin's mission to Naboo is his first in AOTC. It would also rid us of that 'jealousy' angle that is kinda there but goes nowhere.

A little correction I have to make (though no one will care :P): the Neimoidians DID send TC14 away with drinks before they received the order to kill the Jedi from Sidious: http://www.youtube.com/watch?v=joTzwjVUSo4

Guess RLM was wrong on that one, but then again, he couldn't even tell two handmaidens, who were mentioned by name in the movie, apart.