I guess this comes from me seeing Firefly first, but Mal will always be the main character. I don't even have to explain why he is in the TV series because there's no argument there. In the movie, Nathan Fillion gets top billing both in the opening and closing credits, and the movies posters/DVD box. While that's stupidly not always indicative of the lead character (what are some movies thinking?!), I feel that it is here. When we first board Serenity, we follow Mal through the ship, introducing us to all the characters. Joss even filmed an additional scene between Mal and River, right before they get off at Lilac, to make it more obvious to the viewers that River, who up to that point could have been mistaken as the lead character, "passes the movie off to Mal." All the confrontations with the Operative are against Mal, including the final battle. The two scenes with Shepherd Book are opposite Mal. He gives two big monologues to the rest of the cast, including River: the, "I'm not waiting around for the Alliance to choose mine," speech and the, "I aim to misbehave." And at the end of the movie, we once again follow him through the ship, talking to the Operative, Zoe, Inara, and, finally, River.
I'm not trying to diminish River's importance in the movie, but Mal is, and always has been, the hero, the protagonist of this 'verse.