The goal would be to remove detritus over a large span of the substrate. Ultimately, you want to get as much of it out as possible. But, the bigger problem with the method you described is that there would only be a "suction" if the bottle is upright (hole at the top), which wouldn't pull in the detritus from the substrate level. The reason the bottle method works when full of sand is that as the sand falls out of the bottom, it creates a void in the bottle and the pressure difference between the bottle and the water causes the water to shoot into the bottle. So, unless by "empty" bottle you meant truly empty (vacuum), you wouldn't get anything off the bottom of the tank.
The goal with a water change, besides removing water (and nitrates, etc.) is also to remove the detritus from the substrate, and collect some water to rinse the filter media off to keep the filter working at an efficient level. For me, speed is not a factor at all. During the water change process, I get some "me" time and I get to study the tank closely, inspect the fish, etc.