Milano will help, but he won't solve the issue. It's a scheme problem.
Buffalo will give up the runs to the second level. The problem is that if a RB can break contain on the 2nd level they can break off a huge run. Go back and look at the big runs, its almost always a clean hole where an RB can get some momentem and then run past a linebacker to the secondary and it becomes a foot race.
Its really just a trade off, big runs like that are rarer than big pass plays, and teams need more to go right for it to happen. Its frustrating, for sure. But overall success of the defense suggests its the proper decision.
I would argue that it is a scheme choice and not a scheme problem.
There is no defensive scheme that can take away everything that a quality NFL offense wants to do. The Bills defense is designed to take away explosives in the passing game first and foremost. That is why they have played nickel about 80% of the time, dime about 20% of the time, and rarely played with either 3 LBs or with a heavy box.
The Bills D is 7th in Points Allowed, 7th in Passing Yards per Attempt, 4th in INTs, & t-5th in fumbles recovered.
Because they play so much nickel and dime and they play so many light boxes and dare teams to run against them, they get gashed in the running game when they make alignment and/or run fit mistakes. But, that is the gamble they are willing to make in order to make it really hard to get explosive plays in the passing game.
They are making the bet that explosive running plays are rarer than explosive passing plays if they were to take Taron Johnson off the field and play a 4-3. Or, if they were to load up the box against the run on a more regular basis and give up more on the backend.
And even with all that, the Bills have only given up 6 rushing TDs this season (tied for 3rd fewest in the NFL).
They give up a lot of yards per carry (t-3rd worst at 4.8 YPC), but they have been good at stopping the run in the red zone and not giving up rushing TDs.
At the end of the day, I'll take a defense that is pretty good at taking the ball away, not giving up a lot of points, and has been solid when needed for the most part (red zone & second half).