I personally believe the Merovingian and Persephone are former neo and trinity characters from a past version of the matrix, when neo is given the choice of saving zion and taking the architects deal or dooming all of humanity to save trinity the past versions of him took the deal and selected theyre mate as one of the 12.

There is def mysticisim in the movies such as Neo rising from the dead in the fist movie some of the pons essay post. I think the main beauty of the movies is everybody has a different view on it and only the writers can say what they truly meant, the rest is guess work.