A few comments on this:
1) Overall, I like the alignment. Still not a huge fan of using Queen, but it's pretty well done.
2) The direct connection to the Cherry ROW is a big deal. In the previous iterations, I was strongly suggesting an extension of the ROW, either surface or tunnelled, to connect to the DRL station around Queen & Parliament. Now that it's even south of King & Parliament, that "gap" no longer exists. This will take a huge load off the QQE ROW, as Portlands and Distillery-bound traffic will be split between QQE and Cherry.
3) The only thing I don't like is both downtown stations facing 'into' the loop instead of 'out'. IMO, coverage would be much better if they had both stations with ends at Yonge and University respectively, but extending out towards Victoria and St. Patrick. Everything inside of the loop is already very well connected by the PATH network, but extending the stations boxes outwards from the loop effectively extends the walking radii of both Queen and Osgoode stations. Looking towards an eventual westward extension, having Osgoode extending to St. Patrick puts having a Spadina station between Spadina and Peter a real possibility, which effectively makes the entire stretch of Queen between University and Spadina easily walkable to the nearest station.