I guess what seems so bad about padding are several points, above and beyond the obvious fact that trains end up running A LOT slower than they have to.
1. The padding seems to make a mockery of many mid-route station stop times. A train can be hours and hours late and all of a sudden get to the endpoint and miraculously be on or close to on time. I stand corrected by anyone on this forum if I assert that I can't imagine that the pre-Amtrak passenger trains had anywhere nears the padding that the Amtrak LD trains, and I guess even some of the shorter distance trains, have as part of their schedules.
2. The padding seems to indicate just how manipulated Amtrak is at the hands of the freight railroads. If some trains are coming into intermediate stop stations consistently ahead of schedule, what possible reason is there for the schedule to year after year continue to have the same padding unless Amtrak is so incredibly weak in contrast to the freight railroads that the system just acquiesces year after year to the ridiculously slow schedules. Is Amtrak so cravenly prostrate and on its knees to the freight railroads that it never tries to get the schedules alterted to reflect current reality?
Or is the reality so disgusting i.e. that the padding allows the freight railroads to shunt Amtrak LD trains to the side for their freight trains, that the padding ends up the elephant in the room that no one wants to talk about, that Amtrak is for people either too poor to travel by plane (so they go in coach) or for people who love railroad travel so much that they will put up with and excuse almost anything that happens to Amtrak or for people who have so much time on their hands and have already figured that Amtrak delays are simply part of their time wasted calculations.
No matter how you slice it, the larger perspective of the padding leads to some pretty discouraging thoughts about the status of the Amtrak system.