I agree with both arguments. Speed through Sq.1 should be made as smooth as possible, but at the same time I hear about the future importance of Duke of York - yes, it's got a great future ahead of it with a little smart planning. If enough balances, investments, political will, and sacrifices can be made, I can see a design solution for having LRT service go by Duke of York.
It would only really work if the political will exists to abandon both the GO and MT existing terminals, and I am doubtful that such a will exists, but if a new joint-terminal is built at Princess Royal Dr. and Duke of York, on the east side of Duke of York and spanning both sides of Princess Royal Dr., and on two levels, it could provide of good design solution.
The LRT could duck very breifly underground on Hurontario south of Elia to cross the southbound Hurontario traffic lanes, come out alongside the south edge of the westbound 403 onramp from southbound Hurontario, continue ascending, up over the 403, and then descend into the grassy space between City Centre Dr. and 403 (this would be a prime spot for turfed-track), and then ascend the LRT again as Duke of York approaches while City Centre Dr. road traffic lanes descend, and the two LRT tracks could then spread out and descend onto Duke of York at the far lanes closest to the sidewalks. Road access to the commercial properties from Duke of York between Rathburn and City Centre Dr. need to be re-located to a point further south and with some turning restrictions.
Service an LRT stop at Rathburn, and from Rathburn southward allow bus traffic to share the dedicated lanes with the LRT. Re-locate the Sq.1 parking access road between Prince of Wales and Rathburn to use the space freed up by the existing terminal at the end of the project. Grade-separate Prince of Whales from Duke of York (except the sidewalks, where present), with Prince of Wales going underneath Duke of York.
Now here's where it starts to get funky, it's a little hard to follow but use your imagination: Take the southbound/west-side Duke of York track (closest to City Hall) underground through a portal spanning between Prince of Wales and Princess Royal. Service the transit terminal by LRT at the south side of Princess Royal beneath Duke of York (passengers detrain on the east side of the southbound LRV). Meanwhile, the northbound/east-side Duke of York track (closest to Sq.1) stays at-grade, but at the Burnhamthorpe/Duke of York T-intersection, grade-separate the westbound Burnhamthorpe lanes only (except the inner-most/south-most lane for the LRT and bus traffic), and the northbound Duke of York lanes (except the out-most/east-most lane for the LRT) to allow right-turns onto Duke of York by cars coming from the east (travelling west) along Burnhamthorpe. Swiggle the Burnhamthorpe automobile lanes one lane-width south while passing beneath the LRT track and left-turning surface to/from Duke of York/Burnhamthorpe (eastbound lanes) to allow space for a lane to turn right onto Burnhamthorpe from Duke of York (enabling a south-to-west turn) by having the outer-most/north-most lane on Burnhamthorpe west of Duke of York be non-grade-separated, bringing the other lanes back up about midway between Duke of York and Living Arts Dr.
The northound LRT stop services the new transit terminal at-grade, while the cross-track traffic from the southbound stop is grade-separated and prevents pedestrian traffic from interfering with LRT service, and allowing grade-separated left-turns for buses bound for the new terminal. The LRT stop is in the most strictly technical sense "outside" the terminal proper, but with sheltered access directly to it immediately beside it acting as an "extension" of the terminal proper.
The southbound/west-most LRT track stays underground until it has turned south-to-east onto Burnhamthorpe, immediately after which it rises. After serving a stop at Kaliya Dr. on Burnhamthorpe, it would descend again to make a grade-separated turn back onto Hurontario. It would serve an underground stop immediately after the turn and then rise to the surface by Elm Dr.
This should provide very smooth service through the area with negligible time impacts as the right-of-way dodges many traffic signals and is a mix of exclusive and semi-exclusive. It serves Sq.1 and MCC proper equally, and keeps an acceptable service design for the Transitway with the new grade-separations on Duke of York plus dedicated lanes shared between bus and LRT.