The answer is really obvious; the impact on car traffic.
In Downtown Hamilton, one lane will be available for cars in both directions (between Mary and Wellington there is only enough space for westbound traffic). In addition, there will be no space for parking along King Street which causes opposition amongst business owners.
In Mississauga, there will be two lanes available for cars in each direction, even in Mineola where there are currently four lanes. Where Hurontario crosses the highways (with the exception with the QEW) there will still be six lanes. There's also no parking to deal with, as it isn't permitted in the first place and businesses have their own parking lots. That's why the Main Street portion got shot down, drivers were too inconvenienced.