A few observations to start:
A character can have but one magical focus. I think that this is a great rule for balance and for keeping characters unique.
I and at least one of the other posters on this board (I think that it was either Xavi or Gribble) make it a point to encourage all magus characters to take a magical focus because they are so darn cool.
The published example mystery cults are packed with initiations that give characters specific magical foci
Magical potency has a significantly different feel than magical focus. Bringing the mystical associations of natural material to bear in your spell casting with potency rather than pure magical horse power of a magical focus.
Although I've never encountered this problem in play; I could foresee a situation arising where a character who has a darn cool magical focus wants to undergo initiation in a mystery cult but all of the players involved realize that having the character loose their old focus in favor of a new one would make the game a poorer and less fun experience. The by the book resolution to this situation is to experiment with the script and get the character something different. I'd prefer a different option, so I'm putting up a possible house rule (despite the fact that my last game ended in April and I don't think that I'll start a new game until, at earliest, August). Here's the rule:
When a character who has a magical focus through some event, such as a mystery initiation, would gain a second magical focus, rather than loosing the first magical focus in favor of the second the character gains a new virtue with the same scope as the new magical focus but with different effects. For example a character who has a magical focus in rivers joins the Confraternity of Roland and undergoes initiation to gain a magical focus in swords. Rather than loosing his river magical focus virtue he gains a new virtue with the scope of swords. Example virtues are below:
Magical potency: As described in Mystery cults and Mysteries revised
Magical connection: The character gains a +3 (minor) or +6 (major) bonus on all casting totals or lab totals involving the subject of the virtue. Also, when casting spells that involve the subject of the magical connection the caster acts as if he had the life boost virtue and the life linked spontaneous magic virtue. Finally the caster may incorporate the following effect modification into any enchantment that he creates within the scope of the magical connection: physical empowerment, 2 levels, when the creator of this enchantment triggers the power (and only the creator) he may sacrifice fatigue levels , each fatigue level sacrificed increases the effect's penetration by 5 points.
Magical facilityThe character gains a +3 (minor) or +6 (major) bonus on all casting totals or lab totals involving the subject of the virtue. Also, with magic that falls within the scope of the magical facility virtue the character gains the benefits of the virtues flawless formulaic magic and cautious sorcerer
Magical adaptabilityThe character gains a +3 (minor) or +6 (major) bonus on all casting totals or lab totals involving the subject of the virtue. Also, with magic that falls within the scope of the magical adaptability virtue the character gains the benefits of the virtue flexible formulaic magic formulaic magic. Finally the caster is able to effect spontaneous magic and enchantments that fall within the scope of the magical adaptability with muto vim spells as if they were formulaic spells.
Magical controlThe character gains a +3 (minor) or +6 (major) bonus on all casting totals or lab totals involving the subject of the virtue. Also, with magic that falls within the scope of the magical control virtue the character gains the benefits of the tamed magic virtue. Finally the caster may incorporate the following effect modification into any enchantment that he creates within the scope of the magical connection: boostable,2 levels per pawn , when this enchantment is triggered the triggering character may sacrifice one or more pawns of vis to increase the power of the effect. Each pawn sacrificed increases the range, duration or target of the effect by one level. One pawn can be sacrificed to empower a particular casting for every two additional levels added to the enchantment's effect.