Toward the end of Leo's tenure, there was talk that he couldn't relate to younger pitchers, specifically Marquis and Spooneybarger were named. However, he at least had a track record over time in dealing with younger pitchers.
It seems like the magic that Dave Duncan worked tended to be with veteran pitchers, as well, esp. if there had been at least some previous success. In Oakland, that was Dave Stewart and Bob Welch. Maybe it's a personal thing, but it always made me wonder what the exact cause was of the total regression with Todd Van Poppel. This guy was next in line among Texas fireballers after Ryan, Clemens and before Kerry Wood (but carrying A LOT more intial hype). Yeah, there was an injury, but the kid never recovered and developed into anything close to what he was supposed to become. IIRC, on the downside of his career, he was a reliever with the Pirates when nobody wanted to go to Pittsburgh.
Somebody messed up that situation in a very big way. It's not to specially single out Duncan, but that had to have reflected negatively on the A's org. The Braves didn't have any pitching prospects of that stature (ie #1 overall) during that era. So, there's no point of comparison. Glavine & Smoltz were highly regarded but not advertised as staff ace material, let alone future HOFers, when they were moving through the system. Avery, Llliquist and Mercker even had higher draft positions. Of that group, Avery was the one who was most considered "can't miss" from draft through major league debut.