Call him the main character, the lead, the hero, the player character; most every good story has a protagonist. He (or she) is the person we follow. Either because they provide the viewpoint and let us into the world or because they’re out on a grand quest. A lot of stories rise and fall based on the protagonist (or lack thereof).
The lack of a protagonist in The Phantom Menace is one of its shortcomings. Obi-Wan would make a great one, only he winds up playing second fiddle to…well, everyone for much of the film (and sits out all of Tatooine). What about Anakin? He doesn’t get introduced until Tatooine and has no character arc (what’s his motivation?) beyond being the kid who wins the podrace and blows up the droid control ship. Heck, he hardly does jack on Coruscant.
Padme, then! Only she doesn’t do much of anything (besides the senate thing) and her duplicity as to who’s actually her and who’s a handmaiden hamper our getting into her as a main character.
Fine! Qui-Gon! He’s awesome, he gets the plot moving, he can be the protagonist, right? Only no. He plays the mentor archetype, the one who guides the protagonist along. Qui-Gon is a static character who guides the plot, but has no personal investment. Plus, at the climax, the duel with Darth Maul is (sad to say) completely irrelevant to the plot.
Basically: there’s no protagonist in The Phantom Menace, no one for us to root for besides the umbrella of “the good guys”. It hampers our investment in the story. It worked for The Empire Strikes Back because we already had our investment in Luke and Han from A New Hope, but in the latter Luke was unquestionably our viewpoint character and protagonist. Menace has no such luck.
Not to say having a clear protagonist means we’ve got a good story on our hands. Let’s look at Twilight (having read a crappy book makes for good examples). Bella is unquestionably the protagonist, but she lacks anything that makes us care. She has no motivation past getting Edward to fall in love with her. She’s boring and has little characterization/use besides being an avatar for the reader. If the protagonist has no proper characterization, arc, or motivation it becomes hard to get invested.
Look, a work doesn’t have to be high art to have a protagonist. Rod, from Hot Rod, is an example of a great protagonist. Does he have characterization? He’s a delusional, hubristic wannabe stuntman, so yes. His arc is to get the girl and save his stepfather’s life so he can kick his ass. Why? Because he wants his stepfather to respect him. Yes, Hot Rod is a (hilarious) stupid film, but there’s a clear protagonist. It works! The Princess Bride has Westley and Buttercup as protagonists and Fezzik and Inigo as deuteragonists. Escape from New York has Snake Plisskin, Final Fantasy VII has Cloud, Chuck has Chuck.
But what about ensembles? Shows like Firefly, How I Met Your Mother, and Lost; who’s the actual protagonist? That’s the beauty of tv, supporting characters can all get their spot in the limelight. An episode like “Ariel” has Simon as one of the primary protagonists, or “The Constant” has Desmond as its protagonist. Several protagonists are far easier in an episodic serial.
Now the big question. The Avengers. It’s got seven main characters (Captain America, Iron Man, the Hulk, Thor, Black Widow, Hawkeye, and Loki). Who’s the protagonist?
They all are. Each one has their character arc and/or motivations (Loki wants to go home, Iron Man grows into a hero, Hawkeye wants to make up for what he did, etc). With or without the prior movies, each protagonist is set up in The Avengers and winds up as a realized character. You can call any one of them the lead (well, maybe not Hawkeye [it’s workable, but definitely a bit of a stretch]), and the movie still works. You can have multiple protagonists, so long as they’re actually protagonists and not a cast of supporting characters.
It feels like it’s the obvious thing. Stories need not just a protagonist, but a good one. Motivations, characterization, an arc and all that. A good protagonist can help even a mediocre plot. Somewhat, anyway. Y’kinda need the whole lot to tell a good story.
But you already knew that.
Also: buy my book In Transit! Each story has a clear protagonist!