Countering MKs aerial attacks is easy when you practice. Just dodge and hit.
But here's the trick: dodge slightly (and I cannot stress that enough) before you normally would. Too early, and you look retarded and get your ass handed to you. Too late, and you look stupid and get your ass handed to you.
After the dodge, he'll probably try to strike again, so go with another dodge. This way, if he doesn't attack, then he definitely will after this dodge. That's when you use counter.