It is really a great question, because it is really hard to answer! Your thoughts? What do you think?
Amidala's and Anakin's stories, seen through the eyes of Qui-Gon and Obi-Wan. But the main lead is, in my opinion, Qui-Gon. The second lead is Obi-Wan.
Who is the main character of MASH? Gosford Park? Fellowship of the Ring? The Avengers? Some films are ensemble pieces.
Qui Gon. I find it funny considering quite a bit of story and art was made with Obi Wan as the lead who goes to Naboo by himself but GL decided he wanted Qui Gon. I think this was a good thing as Maul wound up with a kill that then made Obi Wan killing Maul more of a big deal.
Anakin's story is a subplot; Obi-Wan is a sidekick until the duel. Weird how you picked Fellowship of all, considering how that was the one with Frodo as the sole, central protagonist. The next ones split them up, and shifted to Sam's PoV as well. Two main characters: Amidala and Qui-Gon. Amidala is the protagonist of the Naboo plot, Qui-Gon leads from that to the background conspiracy behind it. "She's the leader of the doomed town, he's the knight errant who protects it." - the arcs are complementary, as he takes charge while she's passive, and then gradually shifts his focus towards the Sith and the Prophecy while she gradually turns proactive and takes control. Obi-Wan is a sidekick and a bit of a foil, but becomes his co-protagonist during the duel and eventually takes up the mantle. Anakin is a supporting character, complemetary protagonist in the Tattoine subplot (where Padme takes a backseat), and gets a supporting role in the final heist.(though the biggest climax). It's all quite simple.
I think the most important characters are Qui-Gon and Padme Amidala. If Obi-Wan and Qui-Gon switched places on Tatooine he'd be less of a sidekick.
Since four or so days ago, I have believed, thanks to the popular reddit post, that Jar Jar is probably the Phantom Menace. Rhymes with Luke as the New Hope. Jar Jar is the protagonist.
I would say,Obi Wan,Qui Gon and Anakin. I did not counted,but I think,Qui Gon is shown most of the time,on the screen and 2nd is Obi Wan and Anakin.
Well he certainly gets a lot of screen time. And even gets his own arc (more than Obi-Wan for sure). I think had GL toned him down and made him more serious he would have been received much better.
It's Padme, who has the biggest, if not necessarily most visible, character arc in the film. She goes from putting all of her trust and faith into those who advise her to ultimately making decisions for herself in order to liberate Naboo. The problem is that her arc isn't quite fully emphasized as much as it should be, and definitely takes a backseat on Tatooine when Anakin enters the film (although her verbal sparring with Qui-Gon plays into her developing mindset). I think the reason Qui-Gon is pointed to most often as the main character may have to do with screen time and the fact that he is the film's strongest anchor, but his character doesn't develop or change too significantly.
My theory is that Lucas thought he could duplicate the success he had with Yoda, but didn't realize that people would ultimately be annoyed by the character. He was never able to make good on his intended plot twist. Jar Jar is annoying, but watching him is fascinating. Think of him as the protagonist and the whole movie changes. But it does clear up the confusion. If not for Jar Jar, I'd say Qui-Gon is the protagonist.
What was the intended plot twist? Anakin killing his childhood friend? I think some fans would have loved for that to happen. Jar Jar is a classic Fool archetype and some of his lines are actually funny. He could have been a pretty good counterpart to the stuffy Jedi had Lucas tweaked things some more.