The Epidemic-shuffling instructions in the Pandemic rules seem to sort of lower the odds that two Epidemic cards are ever adjacent:
Divide the remaining Player cards into a number of piles according to how diﬃcult you’d like to make
the game. Make the piles as equal in size as is possible.
Shuﬄe an Epidemic card into each pile. Stack the piles on top of each other to form the Player
Draw Pile. (If the piles aren’t exactly the same size, stack them so that the larger piles are
above the smaller piles.) Put any excess Epidemic cards back into the box.
This will obviously spread the Epidemics out throughout the deck, but my group also interprets "shuffle into" to imply that we shouldn't let the Epidemic we're putting in each pile to end up on the top or bottom. As long as the Epidemics are somewhere in the middle of each pile, you won't get two in a row. Although you might get two very close together and it certainly does suck when that happens.
Setting the deck up in this way will guarantee you don't get a double-epidemic.