I think Yost's biggest flaw is that he often manages based on what he'd like to happen, rather than what should be expected to be the most likely outcome. He really believes in his players, which is admirable to a point, but it sometimes costs his team. This is particularly glaring with pitchers, where a guy is clearly gassed, but Yost always tended to leave them in for one batter too many, hoping the guy would be able to perform an escape artist trick.