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Protecting prospects makes for difficult decisions Reporter @JonathanMayo
To protect or not to protect, that is the question.

It's unclear whether 40-man roster decisions would have shaped Shakespeare's writing, but all 30 organizations just finished going through the process of deciding which Minor Leaguers to put on their 40-man roster and which to leave unprotected -- thus risking losing them via December's Rule 5 Draft.

Players first signed at age 18 must be added to 40-man rosters within five years or they become eligible to be drafted by other organizations through the Rule 5 process. Players signed at 19 years or older have to be protected within four years. Clubs pay $50,000 to select a player in the Rule 5 Draft. If that player doesn't stay on the 25-man roster for the full season, he must be offered back to his former team for $25,000.

In recent years, teams have done a much better job of evaluating and identifying talent, with few Rule 5 picks becoming impact players like Josh Hamilton or even Joakim Soria. Some do stick with their new teams, but most are returned, and those who do stay tend to fill secondary roles, at best.

A big reason for that is the extra year teams have to evaluate. It used to be that the 19 and over set only got three years, with the younger group getting four. That has led to less diamonds in the rough slipping through the cracks.

"The extra time has not only afforded teams more evaluation time, but it also has allowed the natural attrition process to be part of the decision," Indians vice president of scouting operations John Mirabelli said. "Consequently, teams are making much better, more precise roster decisions. Scouting the opposition is important, but knowing your inventory is critical and teams are capitalizing on the extra year."

That doesn't mean that all teams were faced with easy decisions at Tuesday night's deadline. Chris McGuiness of the Rangers, for instance, is fresh off winning the Arizona Fall League MVP Award after leading the elite prospect circuit in RBIs. But Texas took the chance of not protecting him in the hopes that Double-A first basemen aren't always the first order of priority in the Rule 5 Draft.

By and large, teams protected those on their Top 20 prospects list who were in line for making the 40-man roster. There were some exceptions, as well as some intriguing non-Top 20 guys who could be had in December. And it does stand to reason that the deeper a team's farm system, the more difficult the decisions may have been. Case in point, the Rangers not adding McGuiness.

Josh Zeid, Jason Stoffel and Marc Krauss are not currently on the Astros' Top 20, but that by itself signifies how far that system has come. Zeid and Stoffel are hard-throwing relievers and Stoffel had 27 saves in Double-A in 2012. All three were obtained in trades, and it's not uncommon for a team to protect those kinds of players to show they got value in deals, but Houston's depth has improved so much that it was decided there wasn't room for those three.

The San Diego Padres also are thought of very highly in terms of their Minor League depth. They made the decision to protect Jaff Decker's bat, though he's dealt with injuries of late, over second baseman Jonathan Galvez, though the Padres hope they get to retain the infielder, who has hit .281/.375/.435 in his career.

Mirabelli's Indians chose not to protect first baseman Jesus Aguilar, who was No. 11 on their Top 20 list, after a solid yet unspectacular 2012 season that saw him reach Double-A for the first time.

While many performers in the Arizona Fall League earned spots on 40-man rosters -- lefties Kevin Siegrist of the Cardinals and T.J. House of the Indians are two examples -- McGuiness isn't the only one who wasn't able to turn a solid performance into a roster spot. Kyle Kaminska, who came to the Pirates from the Marlins, along with Gaby Sanchez, in a Trade Deadline deal, finished third in the AFL in ERA, but the Bucs decided there wasn't room on the 40-man for the right-hander.

Jonathan Mayo is a reporter for Follow him on Twitter @JonathanMayo and Facebook, and listen to him on the weekly Pipeline Podcast.

Jonathan Galvez, Kyle Kaminska, Marc Krauss, Chris McGuiness, Jason Stoffel, Josh Zeid