I agree that a Wellington alignment is the best option and the article does a good job of laying out why. The real fool with regards to this article is the city as a whole... it drives home that DRL planning is still working on answering questions that should have been sorted out years ago!
The Wellington alignment serves the Financial Core extremely well, while still being close to offer walking-distance service to Southcore and all the big attractions (ACC, MTCC, SkyDome). Something that wasn't so focussed on those trip generators with heavy peaks seems like a good idea, but it is those heavy peaks that overwhelm the Yonge line and can best utilize the relief.
The article downplays the importance of serving Union. I disagree (sort of). Union will still be the hub of the network, express and intercity trains aren't likely going to serve those extra DRL connections at the Don River or elsewhere, not all GO lines will intersect the DRL, and buses at the Union bus terminal aren't going to make connections elsewhere. That said, I think a Wellington alignment DOES serve Union. The walk from Wellington to Front is only 170m (about 2 minutes). I've walked longer making train connections before... I'm sure the walk from Bonaventure station to Gare Centrale in Montreal is longer!
The TTC has said they need to rebuild the Union station streetcar loop. This raises the question: if the DRL goes along Wellington should the loop be rebuilt NORTH of Front Street, to provide a connection to the DRL?
Overall, as much sense as Wellington makes, it does make sense to assess the cost of the different corridors and weigh the benefits and costs. There is room in the Union Station Rail Corridor from the foot of Church St to about Eastern Ave. The Network 2011 DRL routing planned to utilize this corridor. It might not the as optimal, but if it's a fraction of the cost it should be considered.