Majora's Mask coming before Ocarina of Time wouldn't have really made sense, because Majora's Mask improved upon what Ocarina of Time already did. Had they been released in reverse order, in addition to it not making sense story-wise, Ocarina of Time would have had to build upon what Majora's Mask was.
I think a bigger contributor to Majora's Mask being in Ocarina of Time's shadow is when and how it was released, regardless of whether or not Ocarina of Time came out first. Majora's Mask was released on an additional N64 peripheral that was not largely adopted at the end of the N64's life, the same year that the PS2 came out and the year before the GameCube came out. Had they delayed it to the GameCube, perhaps, it might have been given a more prominent place in the spotlight. People in general might have appreciated it more for the graphics as well, since they would likely exhibit what many think of as a more "Zelda" style than what The Wind Waker offered on that level of graphical fidelity.
The idea that Majora's Mask in the shadows doesn't seem to apply much around here, come to think of it. A lot of ZD's members acknowledge Majora's Mask as an improvement on Ocarina of Time, and many even say Majora's Mask is their favorite Zelda game.