You understand that this game is played by humans, right? Humans who react to decisions and situations in a human way?
It's all well and good to say, for example, that a manager should bat his best hitter second in the lineup because there's evidence to support that decision, but it's another thing to do it and get a player to buy into it. Whether we like it or not, the "best" decisions in theory may not always be the same in practice, in part due to human behavior.
For example, would you rather have a sulky Bautista hitting second who is unhappy because he thinks he filling a slap hitters role, or would you rather have a confident Bautista who is proud of hitting in the spot that many think is reserved for the best hitter on the team?
I think a good manager in today's game needs to provide a balance between the archaic Jim Leyland type guys at one extreme, and the computer toting guy at the other extreme. In my opinion Gibbons does a pretty decent job of finding that balance. I would keep him personally. While I think there's a chance they could find somebody better than Gibbons, I feel like they are more likely to find someone far worse.