I really want to like this game, but it seems the makers do everything in their power to make it challenging before play even begins. The rulebook is as confusing as the videos on YouTube.
 
For example...on page 6 of the rulebook under #3 Domains
"Each player takes three cards that are not being used in this game and places them face-down next to his deck."
 
Great...WHERE are these cards supposed to come from???? Is the player supposed to LOOK at these cards or not? If he is allowed to look at them, how should he choose which cards to use? Is it okay to use story cards? Icon cards? Unique cards? Conspiracy cards? Event cards? 
 
C'mon designers, throw us a bone. The rules are supposed to HELP people, not confuse them. We shouldn't need to call in the old gods to decipher rules.   

Jason: You have nailed it! But I am going to withdraw from further comments, replies, or criticism of CoC. Too many folks are obviously enjoying it, and I don't want to be a "downer" on their game. Perhaps in the future they will come out with new rules and I will be able to play and enjoy.
 
Dep

I find it odd that the CCG version of CoC had special cards to mark your domains, but the LCG version got rid of them and instead gave us that board (that nobody uses) to place your story cards on and those cthulhu figures (that are cool, but we usualy just use glass beads instead).

Deputy, I think I understand where you're coming from. One of the fellas in my playgroup is a M:tG player, and he - rightly - bemoans Call of Cthulhu's issues with templating (i.e. inconsistent wording between cards; wording that can be quite similar but means very different things, like "commit" during the normal commitment step vs "is committed" bypassing the normal exhaust to commit step). There's no denying that Magic is a polished* game - they have the years of experience and the budget for extensive playtesting to make sure of it!
The current set of Call of Cthulhu cards stretch back as far as 2006 (with the reprinting of the original asylum packs as the Forgotten Lore cycle), and unlike collectible card games like M:tG, the Living Card Game model doesn't have a format rotation - so that's 8 years of card releases all in one big pool, which unfortunately have resulted in some of the inconsistencies between cards; and FFG only errata when they feel it's absolutely necessary.
In short, you're right to expect more of other card games - M:tG has set the bar high - and to point out Call of Cthulhu's shortcomings. If someone doesn't say something, nothing will change, so good on you for putting your thoughts out there, Deputy! I agree that areas of the rulebook (and FAQ for that matter) could be improved, but it's nowhere near as bad as "Might as well just toss the rulebook and base the whole game on whatever the players want the rules to be."
Answers to tricky interactions can be had - though not as instantly as you might get from MTGO - even official ones on the occasion there's disagreement on the topic between friendly forum users. Most of the forum users who take the time to assist with advice are aware of things like the detailed action timing chart in the FAQ, and can step you through it to determine what would likely be the correct outcome.
If the niggle of tricky interactions is stopping you from enjoying this otherwise great game, and you feel you can't be "flexible" when the questions do arise mid-game, then I'm sad to say that perhaps jhaelen's harsh advice is the right thing for you.
* 'polished' - in terms of consistent templating - is not to say that I think M:tG is the better game. I actually enjoy Call of Cthulhu far more, with its innovative resourcing system, flexible faction combinations, and other challenging decisions.

Jason: You have nailed it! But I am going to withdraw from further comments, replies, or criticism of CoC. Too many folks are obviously enjoying it, and I don't want to be a "downer" on their game. Perhaps in the future they will come out with new rules and I will be able to play and enjoy.
 
Dep

That would be nice indeed.

Actually, I'd wish they had included dedicated domain cards in the core set like they did in the CCG starter packs.

Any three cards you aren't using. You may be over thinking this one. These are just cards to mark your domains and to cover up cards you have resourced, except for the resource icons.

The short answer - both!
 
Secrets of Arkham is being reprinted with x3 copies of each card.  The old SoA had only x2 copies.  Back in the early days of LCGs, a few of the deluxe expansions (mostly from AGoT but also SoA) only had x2 copies of cards instead of 3.  This is the last expansion to be updated into the now standard x3 copy format.
 
I believe the revised version of SoA is due out some time in February, and it will say "Revised" on it so you can tell the difference between the old and the new (I also think it will retail for $29.95 as opposed to $24.95).
 
Did that help?