A lot of questions, most of which don't have solid answers but I'll try:
The city absolutely intends to clean up City Hall's exterior when the entire project is done. An assessment was made around the time that they were finishing restoration of Old City Hall but it was deferred. I don't know where it stands now but I'm guessing that they'll want to have the main attraction -- City Hall itself -- looking like new when they finally cut the ribbon on the Nathan Phillips Square Revitalization some time in 2015.
I don't believe the plans to reclad the walkways made it in. They were never a part of the project but would have made a big difference. Still, the walkways will be decked and furnished and cutouts made to open it to the space below and along sections of the sides facing into the square. At that time, it would make sense to reclad the remaining portions as some of the sections need to be replaced or patched up. The rabbit elevator entrance on Queen/Bay is going to be reclad to match the new buildings so it only makes sense to redo the walkways when that work comes up. I still have hope.
The Queen St. ramp next to Osgoode Hall is staying. I wish they would remove the one on the south side along the Sheraton. That one is a barrier that ruins the sidewalk friendliness along that stretch and is significantly responsible for the Sheraton turning its back on Queen St.
The Sheraton walkway is staying because nobody could agree on who to pay for its removal. One thing is certain: it's heading towards the end of its useful life over the next 10 years and needs to be refurbished. It's a complicated problem but I think the city will have no choice but to fix it or tear it down. Given past statements and intentions, I'm guessing they'd take it down.