Naturally I consider the older Eastern tradition more likely to be true. But I'm curious about how these kinds of traditions develop. Why would French mythographers choose Mary Magdalene over one of the 12?
With Britain I feel there is evidence that a Christian community popped up there in the first century. But with Gaul a Christian community doesn't seem to show up till the second half of the second century. And the oldest one was in Lyon, where it seems the first Christians of Lyon came from Ephesus. Pothinus and Irenaus, the first two Bishops of Lyon were students of Polycarp, who was believed to have been a student of John. And contemporary with them, the Bishop back in Ephesus was Polycrates, who is interesting for a few reasons.
So maybe the later tradition comes from this community of Christians seeing Mary Magdelene as a founder of theirs back in Ephesus?
There are debates about if the assumption that John son of Zebedee is the Beloved Disciple is true. No one doubts the three Canonical Epistles attributed to John were written by the same authors as The Gospel, but the author of those Epistles doesn't name himself either. Revelation is the only John book thought to be by a different author, and only it identifies it's author as being named John.
I've been thinking for awhile about what my position on that is. I'm obviously not for any that say the text has been changed somewhere, so that rules out the Mary Magdalene theory. And I think it is someone probably not mentioned by name in the Gospel According to John, so that rules out Lazarus.
The idea that it was disciple in Jerusalem, usually not involved in what was going on in Galilee I think is viable. If it's the person who owned the house they had the Last Supper in, then that would likely be the man holding the pitcher of water in Luke 22:10.
One thing I've considered is, John was a very common name back then, maybe it was a different person not in the Twelve but also named John? John 18:15-16 implies the Beloved Disciple is known to the High Priests. Acts 4:6 lists a John among the kindred of the High Priests. Also interestingly the Samaritan High Priest during the time of Jesus was named Johnathon, but I doubt that is really relevant.
In a supplemental portion to a post on my Prophesy blog I suggest that it was a different John who came to Ephesus, John the Presbeter.
Polycrates is considered the oldest source on John being the Beloved Disciple. Here is the letter he wrote as transcribed by Eusebius.
"We observe the exact day; neither adding, nor taking away. For in Asia also great lights have fallen asleep, which shall rise again on the day of the Lord's coming, when he shall come with glory from heaven, and shall seek out all the saints. Among these are Philip, one of the twelve apostles, who fell asleep in Hierapolis; and his two aged virgin daughters, and another daughter, who lived in the Holy Spirit and now rests at Ephesus; and, moreover, John, who was both a witness and a teacher, who reclined upon the bosom of the Lord, and, being a priest, wore the sacerdotal plate. He fell asleep at Ephesus. And Polycarp in Smyrna, who was a bishop and martyr; and Thraseas, bishop and martyr from Eumeneia, who fell asleep in Smyrna. Why need I mention the bishop and martyr Sagaris who fell asleep in Laodicea, or the blessed Papirius, or Melito the Eunuch who lived altogether in the Holy Spirit, and who lies in Sardis, awaiting the episcopate from heaven, when he shall rise from the dead? All these observed the fourteenth day of the passover according to the Gospel, deviating in no respect, but following the rule of faith. And I also, Polycrates, the least of you all, do according to the tradition of my relatives, some of whom I have closely followed. For seven of my relatives were bishops; and I am the eighth. And my relatives always observed the day when the people put away the leaven. I, therefore, brethren, who have lived sixty-five years in the Lord, and have met with the brethren throughout the world, and have gone through every Holy Scripture, am not affrighted by terrifying words. For those greater than I have said 'We ought to obey God rather than man'...I could mention the bishops who were present, whom I summoned at your desire; whose names, should I write them, would constitute a great multitude. And they, beholding my littleness, gave their consent to the letter, knowing that I did not bear my gray hairs in vain, but had always governed my life by the Lord Jesus."[Eusebius, Church History, Book V, Chapter 24]When referring to Philip he specifically said he was one of the Twelve. But he doesn't say that for this John who did what the Beloved Disciple is described as doing in John 13:23-25. Just calls him a Witness and a Teacher. The Beloved Disciple witnessed both the Crucifixion and Resurrection.
Side note, some people may think Polycrates here is an early example of confusing Philip of the Twelve Disciples with Philip the Evangelist simply because daughters are mentioned. Philip the Evangelist had four daughters (Acts 21:8-9), Polycrates only mentions three for this Philip. And these three daughters are not specifically described as having been Prophetesses. Paul said all of the Apostles but him were married (1 Corinthians 9:5), so it's perfectly plausible that both Philips had daughters.
On the other hand I myself am not entirety against a theory that both Biblical Philips were actually the same person. No passage mentions both by name together. I get why people assume Acts 6 allows no overlap between the Twelve and the Seven. But remember in John chapter 12 the Philip who is of the Twelve serves as the contact between Greek Speaking Jews interested in Jesus message and the Twelve. So Acts 6 could just be him still playing that role. And Stephen in mentioned first even over one of the Twelve because he became the first Martyr, while when Acts was written Philip's Martyrdom may not have even happened yet. In that context you may wonder why Polycrates only mentioned three daughters? Well he was only mentioning people who died in Asia Minor (or the Roman Province of Asia), maybe the fourth died somewhere else? And it is interesting that for both Philips the traditions about their careers post existing the book of Acts takes them to Asia, though different cities, yet Polycrates knew only one Asian Philip to reference.
Back to Mary Magdalene. Every Gospel but Luke doesn't mention her till the Crucifixion account. In Luke she's mentioned in Luke 8 briefly. This lack of information is probably why it's so popular for writers to fuse her with other characters. Maybe she was married to the Beloved Disciple? And that's why she traveled to the same place that he and Mary the Mother of Jesus did?
You may wonder then why Polycrates didn't mention either Mary? Maybe it was a little bit of Sexism, he didn't mention any women by name, and perhaps only mentioned daughters of Philip as they further back up the citing of Philip. Or maybe given the agenda of this letter he didn't mention people who didn't keep the Passover on the 14th, or at least who he couldn't prove did.
Update August 17th 2017: Another interesting note is that the Tarasque, the monster Martha of Bethany tamed in France according to the Golden Legend, was said to be originally form Galatia, another region in Asia Minor. If you think Fate/Grand Order has something to do with that popping into my head now..... you're correct.