Luigi was the 2nd player charecter so automatically he's been labeled as a side kick by everybody on the net. Then more recent games cement over that side kick idea.
Mario's the main guy in the game because of Peach. It's Peach who sent Mario the letter in M64, Peach who told him to go to Rogueport, Peach who gets kidnapped. If Luigi went instead of Mario it would seem like an affair was happening.
Just think Luigi went with Mario on all the adventures. Like in Superstar Saga.