Broken Base: In the 2e rewrite, there was a very vehement debate about the author's plans for revising the Marduk Society, which reached the point where, amidst the accusations of Creator's Pet and Author Tract, The author of Princess: The Hopeful, which can be quite succinctly described as "The game of playing a genuine White Hat in the New World of Darkness", spoke out against the Marduk Society, claiming that they sounded too White Hat for the setting. Fortunately, when the 2e Marduk Society writeup was made public, it turned out that many of the fears and accusations were unfounded (see Paper Tiger for one example). There's still some debate about the proper "theme" of the Society, but it's not the hugely divisive matter it was earlier in the project.
Moral Event Horizon: Marduk's disciples crossed it in the backstory when they murdered their master to prevent him from becoming a Hope Bringer, because they realized it would weaken their powers.
Woobie Species: You exude a Mind Rape effect despite yourself, you are forced into emotionally abusing your cultists, it is quite possible you are utterly without guidance in the world due to low numbers of Leviathans, and the oldest organization of Monster Hunters in the world want you dead for perfectly valid reasons. It's official-this game has not only made Cthulhu's cousins sympathetic creatures, it has shown them in need of a shoulder to cry on (indeed, that's why they get possessive of Atolls-they're the only people in the world who can talk to a Leviathan like an actual person).
Oh, and we forgot to mention one little detail; Atolls, at least in 2e? They aren't necessarily nice people. In fact, many of them become abusive manipulators who use the influence they have over Leviathans to literally enslave them for their own amusement. It's a lot easier than it sounds, since an Atoll in 2e can cause a Leviathan's Sanity Meter to lose points by scolding them. Of course, this can become a case of Gone Horribly Right for such Atolls... which only drives a Leviathan deeper into madness...