One of the prime issues that faces teams with budding young cores is what to do once the arbitration process begins. The way things work in MLB, the team has an advantage for the first six years of a player's career, but once arbitration hits, things can start getting a little wonky. That's the point the Detroit Tigers are at now with several key contributors.
While the arbitration process still suppresses a player's value, it doesn't mean that guys can't be in line for big raises. Beyond that, those years go quickly, and can lead to a player hitting free agency in the middle of his prime years, making it difficult to keep him around long-term.