I'm in the midst of setting up mysteries-laden characters and envisioning on to insert mysteries material in play, and of course I'd like to immediately put the crunchy goods of TMRE and HoH:MC to good use, which obviously means characters would start having several Initations under his belt, but also risks depriving the Mysteries theme of most of its flavour, so that's how I've thought to deal with the conundrum:
The character starts play with all of his Mystery Virtues (and Ordeal Flaws) "earmarked" for future RP sessions (using a combination of beta-stroyguiding, other players doing Mystagogues NPCs, and bluebooking). Specifically, Quests and Initations ceremonies, as well as deal-dealings and instructions sessions with Mystagogues are earmarked for being RP as flashbacks: think of the way the Bride from Kill Bill or Kane from Kung Fu often flashback to the time they learnt some of their techniques, or the frequent flashbacks Highlander immortals had about episodes of their lives. The rest is abstracted.
Until all of the Initation past mystery stories have been done in-game, all of the experience that character gains from any source, as well as the results from lab work, from current play, downtime, and lab seasons, is "banked" (i.e. it may be assigned as normally, but the effects are frozen). Until the flashback RP "debt" is payed, the character cannot access further experience or lab advances. This is to allow experienced mystae characters to be played immediately, without losing the flavour of RPing the quests and initiations. Two versions of the character sheet should be used, one for playing present-time sessions, the other to record "banked" advancement until it is unfrozen.
Characters are assumed to be established members of their respective cults, and the conspiratorial cloak-and-dagger stuff is cut to the minimum. They know how they stand with their cult, and how to get in touch with it. Mystagogues are assumed to behave a lot like eccentric Wise Old Men and Elderly Martial Arts Masters. The existence of cults is widely know in the order, and the various cults are a semi-open secret. Much like pushers, they often do not advertise (but some do evangelize) but everybody knows they exist, and how to find one with enough effort. Some cults are structured, with degrees of initiations, some are loose affiliations of like-minded mystics and scholars.
A mystery cult lore of 1 is necessary to have one minor virtue. 2 unlocks up to three minor virtues. 3 an unlimited number of minor virtues. 4 allows one major virtue. 5 up to three major virtues, 6 allows all the virtues that the cult may offer.
Rules for integrating Quests and Initiations in apprenticeship and post-apprenticeship character creation from TMRE pp. 19-20 are used.
Characters can generally belong to one or two different cults. For Mystery Cult Houses characters, it is generally possible to belong to one Exoteric (HoH:MC) cult and to one Esoteric (TMRE) cult without special penalties. Ex Miscellanea members have the option of belonging to one Esoteric cult and either treat their sub-tradition as a group allowing up to four Favored Supernatural Abilities, or as a mini-mystery cult offering initations in tradition-related Hermetic and Supernatural Virtues. The free extra Virtues and Flaws that Ex Misc and Mystery Houses characters start with are the effect of apprenticeship and do not necessarily mean full membership in a cult or tradition. For the sake of game balance, characters from other houses may be allowed to join to two different esoteric cults, provided they have fully compatible philosophies and doctrines (ST's call). Conflicting responsibilities and calls on the character's time are to be expected.