Before I begin I would like to say that I am not defending the Phantom Menace. I'm trying to make sense of it. I will explain the plot, who the protagonist is, and why it was made this way.
THE PLOT
What the heck is going on in the Phantom Menace? Blah blah trade negotiations. Blah blah chosen one. Am I right? Here's my take. Mr. Plinkett/RedLetterMedia thought that Palpatine was trying to create a crisis in Naboo so he can become Chancellor, but they failed to understand why he ordered the Trade Federation to do the exact opposite of what he wanted or why the Trade Federation wanted Naboo in the first place or why the Trade Federation even has an army. In the Phantom Menace, Naboo is constantly shown as some kind of nature paradise. Is it possible the Trade Federation wanted all these natural resources to dominate trade in the galaxy? One time we tried to take control of trade. Oh, you might have heard of it, it was called the FRENCH AND INDIAN WAR! Jeez you stupid people need to get your facts right! Anyway, I'm guessing Palpatine purposefully gave the Trade Federation a malfunctioning, half baked army to quench their greed for Naboo and other planets. In return, Palpatine probably asked for control of all their operations so that if they were sucessful, he could control the galaxy through economics. This is why he tells them to do the opposite of what would help his plan because either way Palpatine wins. This also explains why the Federation and the Separatists have the same army : they are both backed by Palpatine. MIND BLOWN! Maybe the reason that all this stuff was snuffed in the movie is to sort of see the story from a child's point of view.
THE PROTAGONIST
Who is the protagonist of this movie? Qui Gon? Wise old sage archetype who wants to train Anakin for the sake of the plot. Obi Wan? Change his name and you'll wonder why he's there at all. Anakin? He's just a little kid! No, the protagonist of The Phantom Menace is... PADME AMIDALA. Think about it. She drives the plot and has a clear goal : to save her people. She has plenty of screen time. She even fits into Joseph Campbell's hero archetype( for the most part )! She's called to action when the Trade Federation attacks, but initially refuses to lead her people toward war. The supernatural Jedi aid her in departing from Naboo. She's plunged into the strange scum filled wasteland of Tatooine, and tested when she votes no confidence against Chancellor Vallorum and convinces Boss Nass to defeat the Trade Federation. She has a life or death situation when she helps fight, but ultimately wins and comes back wiser than before. It's clear thtough her interactions with Anakin that the world is very alien to her, but she grows up in the end. So yeah, she's the protagonist even if she's not a very good one.
EVERYTHING ELSE
Even with all this, the Phantom Menace still has many inexplicable storytelling devices that can only be explained through the Star Wars RING THEORY. The gist of it is that Star Wars was made as a poem using something called Ring Composition. Phantom Menace "rhymes" with Return of the Jedi. Clones with Empire, and A New Hope with Revenge of the Sith. Instead of doing it through theming or story, Lucas decided to do it with images. If you play these movies with no sound simultaneously, you'll find more than a few parallels. The full original article can be found at www.starwarsringtheory.com It will completely change your perspective on ALL the prequels.
tl:dr Palpatine is a genius, Padme is the protagonist, and Star Wars is poetry.