We have stayed on the Gold Floor at both and prefer the Waterfront over the Hotel Vancouver. We found the Gold floor lounge at the Hotel Vancouver very dark and rather small. Because it is an old building the rooms often have some weird layouts and the bathrooms are quite small.The view and the amount of space at the Waterfront is much better.
If you want to be in the very centre of downtown Vancouver then the Hotel Vancouver is a bit better located than the Waterfront. However the walk along the waterfront can be very nice if that is your preference.One advantage of the Waterfront is if you are arriving or leaving by skytrain you can get to the Fairmont Waterfront without ever going outside. It can be handy on a rainy Vancouver day.