One way to protect yourself against these weaknesses is to use a "Peel" technique by the edge rushers.
This page is taken from Wade Phillips' playbook and provides really good details about how this coverage is used against 11 personnel. Below are examples of how it is used versus different formations:
I believe in using a simple defense that employs a limited number of fronts, blitzes and coverages. However, I do believe in having adjustments within your scheme to help protect the "weaknesses" of your defense. Using a "Peel" technique is a great way to help your Mike linebacker play the run more effectively and have low and high hole help versus the pass.