After putting in much, much, much, much more time with Arkham Horror since I originally made this thread, I think the answer is really quite simple:
Shuffle the deck better.
Now, I don't mean to say that you don't shuffle properly or well enough, but I genuinely believe that the real trick is to just shuffle the Hell out of the Mythos deck.
I think the whole point to Arkham Horror is its ability to be completely random. Sometimes a gate is constantly drawn at the same location. Sometimes clues keep appearing at the same location. Sometimes every single Mythos card is unique in those regards throughout the entire game. If every time you play the game you are drawing several Mythos cards with the same gate location, then you're doing something wrong. Here is a solution for when playing with an expansion:
For example, if playing with the base game and Dunwich, do this:
There are 67 Mythos cards in the base game. There are 36 Mythos cards in Dunwich. Lay out ALL the Dunwich cards and make 36 single-card piles. Then, lay 2 base game Mythos cards on top of each pile, except for 5 of them since there aren't enough cards to do so. Stack every pile on top of one another to make your deck. Now the expansion cards are distributed evenly throughout the Mythos deck. Now that you know there aren't massive clumps of base game Mythos cards in the deck, begin shuffling and do so for a solid 5 minutes. The deck should keep fairly evenly spread and make for a much more well-rounded game.
This is what I do every time I play now with an expansion and I think it works wonderfully. I genuinely think that the only real "answer" or "Solution" to the Mythos deck is to shuffle it more than you want to and then some more.
Edit: If my numbers are wrong on the Mythos cards, I apologize.
Edited by BenEggler, 03 March 2014 - 01:52 PM.