bbman,
I pretty much agree 100% of what he posted. I agree with Kyle that distance running is not bad, it is just not optimal. (face it baseball players run a lot so D'Oh they have to run some) Running two miles is in fact good, but if it was me I would alternate between repetitive sprints, and maybe some other longer sprints mixed in for aerobic conditioning. Go back and read it carefully and you will see that he has his son run sprints. .
I don't have the knowledge on the lactic acid build up differences. I have read some of these medical papers in the past, and quickly get lost in the medi-technical terms. To really get the full details you would have to have the whole paper to pick out exactly the test conditions and what he is referring to.
As a practical matter for higher level athletes, these programs need to be phased; a body mass gain phase, an explosive phase, and then flexibility and maintenance phase. I don't think you necessarily have to be getting aerobic conditioning during a mass phase, but I am frankly not sure. My one data point 
right now is in a body mass weight gain phase (lower body primarily) as well as his weighted ball program. He is building his aerobic capacity, again through rowing but I don't really know if he is doing this on his own, or if it is part of his program.
This is not for this thread, but I actually question whether some pitchers should not do summer ball and stay home and workout as they will be better, stronger and more effective if they did this. Again maybe I will open a thread on this for discussion.