Personally, I leave all three Magi in my deck...no more than one has ever shown up in a reading, but Mercury's so fast I wouldn't be surprised to find him in two places at once. They all seem to have different "energies," but I'm at a loss on how to put it into words.
About the primary one - I think one very important thing about him is that he's on tiptoe. The Fool was falling (or floating) in empty space, but the Magus has at least a bit of ground to work with. I also think the snakes around his head form a vertical infinity symbol (all three Magi have it...the most obvious is the eight-armed one, but the wings above the Egyptian-looking one also form one).
I also wonder about this Harald Schulze-Theiler mentioned in the Banzhaf/Akron book...I can't find a reference to him anywhere online, but I'm fascinated by the idea of two "invisible" cards. The explanation they provide involves most number systems being based on 24 (?) of which 10% is often invisible (??). It made no sense to me whatsoever, but I'm wondering if the two extra cards couldn't perhaps be paths to and from Daath, the phantom Sephiroth?