I hate to consume the forum space with complaining, but after a significant amount of playing, I am slowly coming to a conclusion: Serpent decks are just way too good.
I've tried a wide variety of approaches, but honestly, a Serpent deck on autopilot beats most everything but the most fine-tuned strategy, and even then it's very close. It's the ultimate netdeck. There's a bit of strategy to playing it out, but really, not much: you throw the Serpents at the other player, change the icons around as needed depending on what they try to put up for defense, and basically overrun the other side sooner or later.
Generally speaking, the central problem is that the Serpents are very cost-efficient and very flexible (yeah, I know-that's their design feature). They are awash with Terror and Combat icons, and can readily switch between the two, which really helps them dominate the Story phase. Not only that, but they can generate Arcane if needed, which allows them to be used on offense and defense. And they're Cthulhu, which gives them ready access to powerful destruction cards that can sweep the way before them.
The whole set of Serpents isn't completely imbalanced, but there are a few cards which really drive it and make it incredibly effective with little effort, and specifically, they are the cards that make it very cost-effective, too cost-effective in my opinion. If I were to identify a few "problem cards", they would be the following.
Disguised Threat: This allows the nastiest of the Serpents to hit the board on Turn 1. I don't know how that's not a problem. Does any other faction have the ability to put its most powerful non-Ancient One characters into play on Turn 1?
Feathered Serpent: Ridiculously cost-effective, this card will handily win any one-on-one Terror or Combat struggle with little effort, then ready itself with Arcane to be ready for defense. If this gets out on Turn 1, good luck defending against it.
Uroborus: I didn't think much of this card until I really started playing it, but after playing it, well, wow. It's the ultimate anti-destruction card. You can't kill them. Once the Cthulhu player has his discard pile stacked with Serpents, these just keep coming back every time you kill them. It's incredibly annoying. After having played against it, my thought is: did we really need another reason for every deck to have to stack Snow Graves? And that's without Sibilant Cry, which is just the icing on the Serpent cake. (P.S. Is Uroborus supposed to be a unique card?)
There is, admittedly, a fairly straightforward solution to a Serpent deck: the Khopesh. Sigh. They don't pack Toughness, so targeted destruction works. But bouncing doesn't, because they're so cheap; forced sacrifice doesn't, because the Serpent player will just laugh as he sacrifices a cheap Serpent and drops his Uroborus on the board; trying to win in the Story phase doesn't, because it's very difficult to account for all the permutations of icons you could be up against. All that really works is fighting Cthulhu with Cthulhu, and getting your destruction out fast enough to put the Serpents down, or at least until the other side pops them all back out with Sibilant Cry.
I enjoy this game and find it to be relatively well-balanced . . . except for Cthulhu. It's like the designers throw the game balance manual out the window every time they design a Cthulhu card. At this point, even though I'm a rank amateur, I just don't see many other decks making a lot of progress against a Serpent deck, particularly one with the Khopesh and a bit of Shub mixed in to deal with support cards and milling. Maybe I'm speaking too soon, but my strong impression is that the developers let power creep set in with Cthulhu, and it's going to be really hard to put the serpent back in the basket (so to speak) at this point.
P.S. One more point, while I'm ranting: Cthulhu is awash with Deep One and Serpent sub-types, which is one of its hidden strengths. Both Deep One and Serpent traits interact positively with a lot of other cards, but do not interact negatively that I am aware of. One hidden weakness of Yog and Shub is that they have so many Monster and Creature cards, which are vulnerable to various negative interactions that specifically target them. There is not, for instance, any Deep One or Serpent equivalent card to the Sledgehammer. That would make sense if Deep One and Serpent characters were slightly less cost-efficient than Monster and Creature characters; but as far as I can see, they are, if anything, more cost-efficient than their Monster counterparts. It's hard to find a Monster that's as cost-efficient as a Ravager from the Deep or a Feathered Serpent.