1. They are different pitchers. If at every level pitchers are required to pitch complete games, the resulting class of major leaguers will be very different than if pitchers are "babied" at every level. The previous system would have produced more durable and injury resistent pitchers but not necessarily the most talented ones. It's like taking a group of sprinters and complaining that they can't run marathons.
2. Pitchers pitching 9+ innings every game probably didn't go 'all out' on every pitch. Even now, when pitchers are moved from the starting rotation to the bullpen they often say that they like being in the bullpen because they can give maximum effort on every pitch, without needing to conserve energy for innings 6 and later.
3. Games are longer now. Pitching 9 innings over 2.5 hours is likely physiologically different than pitching 9 innings over 3-4 hours.
4. Increased velocity of pitches. Pitchers are throwing at faster velocities and with greater arm speed than they used to. It wouldn't be surprising if this has a durability trade off.