"I believe the flaw in the methodology is that sabermetrics are designed to evaluate individual players, and do not take into account the combination effects of players on a team. In particular, the methods tend to devalue pitching, because it sees the function as run suppression, but ignores the emotional impact that team pitching has on the rest of the team. When pitchers are doing well, holding back the opposition, their teammates feel more confident at the plate, getting more base hits, and more extra base hits. In the field also, position players feel more comfortable taking chances to make great plays instead of taking the safer route. By contrast, when the pitching is poor, hitters become anxious, not wanting to waste an at-bat, often going deep into counts only to strike out or pop up. Fielders are tense, afraid of screwing up, and may not dive after that ground ball or leap for a line drive. The sabermetric guys will look at the season-ending stats and say, “well of course they lost… they failed to make plays, and their OBP was down.” But there is a cause-and-effect relationship between good pitching and good play by the rest of the team."
On top of this person's opinion, you can't measure leadership, communication skills with teammates, value of mentors, emotion, attitude, or effort.