The new proposed challenge system in baseball will fundamentally take away one of the most unique parts of the game, and no I don't mean the human element.
The game of baseball is unique in that arguing calls, and even getting yourself ejected, can have little or nothing to do with whether or not the manager believes the call was incorrect. Arguments and ejections are more often strategy rather than anger. The manager has to defend his players egos as well as pump them up in certain situations.
Bobby Cox was the master of this. He was ejected 161 times over his career (including 3 playoff ejections). Either Cox got inordinately screwed on calls over his career, or he knew a thing or two about motivation.
Enter the proposed challenge system. Suddenly, the manager has to decide whether or not to wave his red flag (I don't know how they'll do it). For getting calls correct, this does have some efficacy. It's far from perfect, but it would mean a decrease in at least some missed calls.
The problem lies, as most things in baseball do, on the hidden side of the game. How is a manager supposed to defend his players within the challenge system. To the player, every call means the world, and when the manager has your back, you know you're right and you know he's on your side. Snap forward to when the system is in place, and all the sudden you have an irate player, whose manager won't even challenge the call.
The outside conflict binds the team together in an "us versus them" kind of way. The challenge system will turn that inward as players are now arguing with there managers to challenge the call.
Another example would be a team who needs a fire lit under their you-know-whats. The manager would love an opportunity to get himself tossed in order to show his team that every play is important and that you have to have dynamite intensity. The only problem is he still has two challenges in his pocket.
What is he to do? Storm the field and argue a call with out challenging it? That rings hollow to the players and everyone else on the field, as a simple ploy. Is he to challenge the call and then argue that the decision handed down from New York is still wrong? The manager has been stripped of one of his coaching tools.
Expanding replay has shown itself to be an inevitability in baseball. The stakes are too high, and everyone at home has the ability to see the play from every angle. The human element only works when there is a degree of vagueness in the crowd.
There is a solution out there, but the challenge system is one which hinders the game by cutting off one of the hidden strategies that makes baseball unique.