The time change for the pere Marquette is cause they found out they can't run the train on the old time table and have enough hours for the crew to get rested and get the train out on time and they're trying to avoid re-crewing the train mid route.
They are only dealing with the SYMPTOMS here not the PROBLEM! If the freights didn't delay things there would be plenty of time for crew rest. Hopefully the new project in Indiana will resolve the actual problem.
Actually, that is the case. Although Amtrak blamed NS and CSX (standard operating procedure for Amtrak), trains that arrived GRR from Chicago on-time were still late leaving GRR the next morning due to crew rest issues. The arriving crew has tasks to perform after arrival before they can go off the clock. The next morning they have tasks to perform prior to the scheduled departure. The schedule simply did not allow enough time for them to do the stuff they have to do and get eight hours off the clock. Sometime in the spring or summer, Amtrak made the decision to eliminate the availability of an en route relief crew for the westbound trip, so absent that, the GRR crew now has to operate to CHI and needs full rest at GRR. The new schedule provides more of a cushion, but at the cost of passenger convenience.