I very much like the mysteries, but Xavi and Fhtagn do make good points.
I agree that there is a rules-creep, at times also a power-creep, and that most mystery cults can work just fine without the mechanics of mystery initiations. However, I actually often like the additional complexity and depth that the new rules provide (e.g the Societetas/Tytalus rules on debate-as-combat sound promising, the guidelines in True Lineages on using Intrigue sound at least like a good place to work from, the Societates/Jerbiton rules and discussion on Etiquette adds volume and content to a skill I would never have otherwise known how to handle, and so on). I also like that the Order is fragmented, that there are secret cults wielding weird powers that sit "behind the scenes", waiting for the PCs to uncover who the REAL power-players are and deal with their bizzare magics.
All of this doesn't make the power-creep better, but I've handled that through some extreme house rules. It does make the rules-creep trobulesome, but I'm easing myself and my PCs into the rules gradually - it's not like we're using all the rules at the moment. I can say that having only specific groups have specific mysteries/powers linked to specific philosophies/concepts helped me define and plan my current saga.
I do disagree with Fhtagn, however. I think the rules work very well as a way to obtain new virtues. I really like the way it works - in order to learn the Secret Seals of Solomon you don't just read a book, you instead travel to the sacred regio at the right time and have a season-long discussion with the angel trapped there.... or something. Much more Mythic, IMHO.
I don't agree that normal Hermetic lineages become impossible. Virtues still get transmitted, through blood (Mythic Blood or otherwise) or by apprenticeship (the Tytalus chapter of Societates wonderfully depicts how the lineage teaches Self Confidence) - and in my saga, House Tremere also has some "mysteries" taught through House Tremere Lore; I can see ones being transmitted even through OoH Lore. This mode of teaching just makes as much sense - even more so, perhaps - than traditional book or one-on-one teaching for gaining Virtues - it feels more Mythic. Non-Hermetic mysteries are still very much possible - from Supernatural Abilities to the non-Hermetic version of Synthemata presented in TMRE.
But the one thing I think Fhtagn is missing is Original Research and Integration of "Ancient Magic". It is entirely possible to both gain and dessiminate new virtues in very Hermetic ways - through lab work, books, and teaching. Presumably, this is how Automata was dessiminated - some Verditius guy taught it to some Bonisagus/research guy, who then proceeded to partially integrate it into Hermetic Magic Theory, producing books that anyone can read to gain the virtue, and and with further integration any magus having it can teach it to any other Hermetic magus.
I actually don't particularly like Original Research as I think the Ancient Magic and Mystery paths lead to much more stories, a more Mythic feel, and a more convoluted (and hence interesting!) social structure. In my saga, if someone would want to pursue this, I intend to dramatically increase the "points-required" of Original Research, and limit it to only supplying very Hermetic virtues (like vulgar alchemy, parma folds, and so on) by itself. I'd allow Integration to lead to initiation scripts for not-so-Hermetic virtues, not to lead to books teaching them to any Hermetic magus - the non-Hermetic virtue is connected to its Lore and mystic tradition, and cannot be directly integrated into plain Hermeitc magic use and practices.
This is how I see a new cult forming: someone wants to obtain a new Virtue, say Pagan Magic. He pursues "Ancient Magic" of hedge traditions - perhaps still extant, so not really "ancient" - that do similar things; in so-doing he picks up some Faerie Lore and gains Insight towards his invention; he finishes it up with some Original Research, and gains the virtue. By this point he has accumulated some strange sources, and some of them provided him with weird takes on Faerie Lore and related abilities; I'll sequester a few of these points to grant him a low score in "Pagan Wizardry Lore". Attempting to Integrate his newfound virtue, he would again gain similar Insight from further XP in this ability, until at the end of the integration he will have not a book describing how to learn this but rather an initiation script telling how to initiate it based on the Pagan Wizardry Lore; alternatively he attempts to create a new script from his current knowledge of Pagan Wizardry Lore, but this is probably more difficult. Thus the new Pagan Wizards mystery cult is born.