I have seen the spread as a problem, but what you are referring to is more of an option spread hybrid, spread offense just means that you spread the ball out, there's no set receivers, however, once you toss in an option quarterback it becomes a real pain in the ass. In the past, the solution has been to hit the QB hard and make him think twice before running, once he crosses the line of scrimage he's just like a running back, receiver, whatever, you can drill him. In 2002, we did that with Dorsey, we made he think real hard before running that football and the result was evident. As far as just the general spread goes, your safeties need to be able to cover tight ends, and your corners need to be able to handle 1-on-1 coverage without a problem.
Todays problem wasn't so much covering the spread as it was spending too much time preparing for the option. We put too many people on the line and as a result you wound up with receivers either 1-on-1 with corners or worse yet, wide open. A lot of teams are trying this and defenses will adapt, but the end result is you have to put the QB on his back and make him revert back to a more traditional style spread offense, ie: remove the running quarterback factor.
With Washington, we did this, we hit Locker hard and made his coach think twice before having him run the ball, one good hit ruins your season. And even more than any other offense, losing your QB means major adjustments for the entire offensive scheme. Not just his arm, but his legs make receivers get open because the linebackers run up when they anticipate the run, so he takes two steps forwards, suddenly your tight end is open in the middle and there's a 20 yard completion. Now if you remove that element, the linebackers don't worry so much, stick to their man and you have a football game.