I'll jump back in, because I did feel like Scotty83's post was very intuitive and geared toward a logical discussion. I appreciate that.
That being said, the fact that a longer-distance run isn't harmful does not mean it is optimally beneficial. Scotty83's post highlighted that sprints of 20-30 seconds increase Vo2 uptake and metabolic threshold. My research, BOF's research, and Kyle's research - as well as what has been provided throughout this thread - echo that claim.
This quote was a red flag for me in Scotty83's post: "I peronaly would rather untrained coaches use a mile run because it requires less knowledge of what they are doing."
If a coach is untrained in the act of developing pitchers, taking the lazy way out does not make things better. He should become educated. If running for an extended period of time is not optimally beneficial, and sprinting is, then pitchers should be running sprints. Coaches should know that.
Even if there is research that says that distance running isn't necessarily harmful for pitchers, there is no research that says it is optimal. Why train in a way that does not maximize your abilities?