My read on this situation is that BNSF is swamped and that there's been enough of a spike over the last few years in traffic in the Dakotas to swamp existing infrastructure. To their credit, none of this could have been foreseen. A few thoughts:
-On rates, BNSF is likely walking a tightrope with the oil shipments: If they charge too much, they'll lose long-term business to the pipeline lobby.
-On investment, I'm not sure how much EIS BS they have to go through, but given some of the stories I've heard over the years (I seem to recall some horror story where ATSF had to fight to reinstall a second track within their own ROW in some canyon), it's quite possible that there are chokepoints they can't resolve in a timely manner.
--It's also clearly the case that they've just been overwhelmed in the last few years. The fact that they went from looking to ditch a secondary main to upgrading it to deal with traffic is a sign of how much things have changed.
--I can't help but wonder if it might not make more sense to re-connect some broken secondary lines in places. Cue the EIS-esque stuff, but it might be necessary if the traffic flow is sustained.
-On dispatching...sounds like they've got an FNG in charge, which works about as well in a railyard as it does in airsoft.
--And while the Builder is "high priority", it certainly sounds like the Builder isn't the only train getting screwed. It's one thing if the Builder is alone in getting the short end of the stick and another if there are hotshot freights
-A thought on Amtrak's front: If they're annulling on that scale, any chance they could reshuffle equipment to at least keep daily service CHI-MSP, and push the "other" train to about 16-18 cars a la the Auto Train so they could move passengers around by a day rather than losing them entirely? If I get cancelled out entirely from a trip, I'll be angry; I'll be less so (more annoyed) if Amtrak does a good job of trying to make it right.