The Chicago Great Western Railway had a direct route between the Twin Cities and Rochester, but much of the right-of-way has been abandoned for around 40 years and taken over by farming.The big caveat with this plan is that Amtrak doesn't build or own its own track, with the exception of the Northeast Corridor between Boston and DC. Instead, it just uses existing freight routes, and there is not (maybe never has been?) a direct route between the Twin Cities and Rochester. So, barring construction of an entirely new dedicated corridor like the Zip Rail proposal, any Amtrak service to Rochester would have to start by going 40 miles east or west to get to Winona or Owatonna before turning north to the Cities.
Would've been nice if they included a MSP-Kanas City service on that map, but if not in the near term then in the long-term it makes sense to have a MSP-Des Moines service that splits to Kansas City and St. Louis.
Also speaking from a long-term perspective, I think MSP-Rochester-La Crosse-Madison-Milwaukee-Chicago is an ideal candidate for high speed rail, or at the very least higher speed rail.