The article is short on specifics, but the Star Tribune reported on Monday that the proposed Northern Lights Express from Minneapolis to Duluth is taking a longer environmental review process that will delay construction of the line by about a year. From what I've learned about the NLX so far, this sounds like the NLX planners are going through a full Environmental Impact Statement process rather than doing a shorter Environmental Assessment.
Some open houses over the summer had display boards with a timeline saying that a full EIS will likely take until early 2012 to complete, while an EA could have been completed late this year or early in 2011. A presentation from the same meetings says that three routes, 9, 11, and 11A, will be evaluated going forward, even though the line from Minneapolis through Coon Rapids and along BNSF's Hinckley Subdivision remains the top choice.
I haven't been able to find route descriptions with as much detail as I would like, but as far as I know, route 9 is the route we've become familiar with, running from Minneapolis to a suburban station (probably at the Foley Boulevard transit center in Coon Rapids), and then heading north-northwest along the Hinckley Sub through Cambridge, Hinckley, and Sandstone before hitting Superior and Duluth.
Routes 11 and 11A would run along the old "Skally Line" from the Twin Cities to Hinckley before getting on the existing BNSF route into the Twin Ports. The Skally Line is largely abandoned today, though the St. Croix Valley Railroad short line still operates a segment. Route 11 would go north from Minneapolis and then cut across to the east from the vicinity of BNSF's Northtown Yard and Canadian Pacific's Shoreham Yard along CP trackage (their Withrow Subdivision) to reach the Skally Line.
Route 11A would instead turn east at Minneapolis Junction and run along BNSF's Midway Subdivision, go past the current Amtrak station on Minnesota Commercial Railway trackage, and go along the CP Merriam Park Subdivision to get to the Saint Paul Union Depot.
I think it's best to go with the current high-scorer, route 9, which parallels the busy Minnesota State Highway 65. MN-65 is not as well known as the roughly parallel Interstate 35, but it has a lot of traffic signals slowing things down and causing driver frustration. I-35 is simply busy in comparison. After route 9 gets built, I think they should consider adding route 11A in as well. Of the three, 11A currently has the lowest score, but it would serve the Union Depot, which is undergoing a major restoration. The Skally Line route also ran parallel to today's Interstate 35 (and I-35E within the metro). It will get harder and harder to justify adding more lanes to I-35, so a train running immediately parallel to the Interstate would be attractive to many people.
A few years ago, it was hoped that the NLX could open in 2012. With the EIS delay and everything else that has added up, it's likely that it will take until 2014 for the train to start running. Fortunately, when it does start up, there should be 8 round-trips per day.