This is actually a fairly complex yet immensely interesting problem and a worthwhile debate.
Elements include: Transitway, GO Transit existing terminal, MT existing transit terminal, Square One, Mississauga City Centre, and Hurontario.
Mississauga City Centre is very inconveniently located as far as being serviced by this corridor is concerned. Its needs would be best addressed by a Burhamthorpe LRT in the future. If such an LRT only goes east of Hurontario, as would probably be expected (i.e. the 76), Duke of York could be such a route's access to the Square One terminal.
The existing terminal is close to the Transitway and that relationship is worth maintaining and enhancing. By association, that includes the relationship with GO Transit.
If the existing terminal's newest addition to the northeast could be maintained, and a new terminal building built over at the next street east of the current terminal building (which is an unnamed street part of Sq.1's parking circulation system), stretching the new northeast addition across the length of the block and integrating it with the existing GO terminal (possibly including grade-separating Rathburn at the current bus terminal and GO bus terminal intersection, assuming the existing MT terminal would be decommissioned after the new one is up), the investment recently made into expanded capacity of the existing terminal would not be thrown away (which is politically important), and maintains a great relationship to the GO services. A new terminal building for MT would also have better direct access into Sq.1 with an opportunity to provide sheltered access all the way into the mall (into the Sears building).
This redesign can accomodate a better alignment option for the Hurontario LRT. It can come in off of Hurontario on Rathburn (and I'd sincerely hope they'd grade-separate the westbound lanes of Rathburn for the LRT to get onto Hurontario at this tricky intersection), tuck down the unnamed street between City Centre Dr. and the current terminal, and then out on Square One Dr. back to Hurontario to serve Robert Speck.
Short, sweet, efficient, and cost-effective.