The Gospels have become so overladen with myth over the past two thousand years that some Christians - me, for example - are not always certain whether an event was added myth, or actually written in the Gospels. And, of course, the Gospels are not exactly gospel themselves, being oral reports written down years later.
I hope I am not the only Christian who thinks that the question of whether Jesus had a special relationship with Magdalene is 1) dumb, since there is no data, 2) uninteresting, 3) a distraction, and 4) irrelevant. What is highly relevant to me is the following scene from John's Gospel, as described by Jean Acocella, who considers the role of Mary Magdalene in her piece "The Saintly Sinner" in The New Yorker:
Magdalene goes to the tomb in darkness, before dawn, and she goes alone. We feel her hurry, her sense of danger. To her astonishment, she finds the stone rolled away. She runs back to the disciples and tells them, “They have taken away the Lord out of the sepulchre, and we know not where they have laid him.” Peter and another disciple take over. They rush to the tomb; indeed, they race to see who can get there first. (This exemplary male competition became a favorite scene in medieval morality plays. In John’s Gospel, it adds a bright little note of comedy to the otherwise dark tale.) When they arrive, they see that the Magdalene was right: the body is gone. They go back home, presumably baffled, but the Magdalene stays behind, weeping. She looks again into the tomb, and now she sees two angels dressed in white. They ask her why she is crying, and she repeats her simple complaint: “They have taken away my Lord, and I know not where they have laid him.” Even with angels, she’s still looking for the body. But then she turns around and sees another figure, who says to her, “Why weepest thou? Whom seekest thou?” The tomb is in a garden, and the Magdalene thinks this man must be the gardener. A third time—it’s like a song—she repeats her complaint: “Sir, if thou have borne him hence, tell me where thou hast laid him.” Now comes the stab through the heart. “Mary,” the “gardener” says to her, and instantly she knows. “Rabboni” (roughly, “My dear rabbi”), she replies, and apparently she reaches out to him, because he says, “Touch me not.” (This is the Latin Bible’s famous phrase “Noli me tangere.”) “But,” he tells her, “go to my brethren, and say unto them, I ascend unto my Father.” He then vanishes, and she is left by herself.
Read the whole piece, which powerfully asserts Magdalene's authority on "matters of the soul."