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His role in the film, with the arguable exception of the unrevealing, disconnected fight with Darth Maul, is entirely epiphenomenal.
Merely because the characters aren't privy to the existence of Darth Sidious, that renders his role subsidiary? That logic makes no sense.
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That's why they call it The Phantom Menace rather than The Palpatine Menace or something like that.
As you are likely aware of, the title of the movie refers to Palpatine/Darth Sidious. He is the "Phantom Menace". That was made explicitly clear by Lucas, despite the already conspicuous connection. He refrained from naming it "The Palpatine Menace" because such an eponymous title is shallow and quite frankly, stupid. So if the title is a direct reference to Palpatine, that must mean the guy is pretty darn important wouldn't you say?
Your argument seems to hinge on the fact that he doesn't have much in terms of a
palpable presence throughout the movie when he adopts the guise of Darth Sidious. That is entirely immaterial. His role is crucial nonetheless, and his appearances--even as a hologram--are plentiful enough.
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The Trade Federation seems to have motives that are explicable to the characters without the need to further investigate the hologram that's somehow running the show.
No, it doesn't. Qui-Gon expresses his bemusement over the motivations of the Trade Federation early on in the film. "There is something else behind all this, Your Highness. There is no logic in the Federation's move here..."
By the end of the movie, they know the Federation was manipulated by the Sith.
Addendum: If I didn't drive my point home before, I'd also like to point out that
Augie's Municipal Band--the title of the victory celebration music that plays at the very end of the film--is
The Emperor's Theme in major key. Gee, wonder why they did that.