Boswell's apologia mentions that Williams is an "average" manager. I agree. That's the problem.
we've talked about his constantly leaving pitchers in to hit for themselves when just about everyone knew they were coming out in the last inning, but the one thing that he really seemed to do in the first half was leave pitchers in too long overall.
Here's Scherzer's pitch counts in a stretch starting on May 1 and ending with his first real bad performance on July 7 (5 ER in 4.2 IP):
96, 114, 94, 104, 110, 108, 101, 116, 119, 106, 100, 105
I looked up Kershaw for comparison:
91, 110, 110, 99, 101, 93, 106, 117, 107, 105, 101, 102, 123
And Bumgarner:
107, 99, 104, 107, 99, 93, 98, 111, 112, 108, 100, 86, 103
So when you look at the numbers, it doesn't seem like was running Scherzer into the ground even though it always seemed like Scherzer was left in too long.