Seth, you effectively answered the question you asked in the second sentence of your article. Baseball players typically don't reach their peak until their mid-to-late twenties, with four to six years of physical and mental development needed. I agree with h20face that Falvey probably did not have a lot to do with establishing Cleveland's system but I think he certainly gained an understanding of what succeeded there as well as how and why it succeeded.
Pitching always has been and always will be the most important part of baseball, but what applies to developing a pitching pipeline also applies to batting, fielding, and base-running. Scouting and player development are the linchpins. Acquire the right players and have a system that enables them to perform at their highest level. This in turn requires acquiring good scouting and player development people.
Falvey has had to essentially rebuild the entire organization from scratch. Fans tend to be impatient and demanding (even fans other than Yankee fans), but in baseball it takes time to do things the best way, and it has been only four and a half years since he was hired. Factor in that 29 other teams are competing for the best people and this is a monumental task. My hope is that in another five years we will have in place a solid pipeline not just for pitching but for all positions.