I have been considering the request and have given it quite a bit of thought.
Some people used to complain that they don't like seeing "WA_" in front of the folder names, so we stopped doing that, which lead to people complaining that they did like "WA_" in front of the names, so we didn't follow through and remove it from all of them. Which lead us to the inconsistancy you point out where some do and some don't now.
Letting each user set their own would be possible, but would hurt the portability, if you were to build a site with your structure and send it to someone with another it wouldn't behave properly, or you might end up with multiple folders.
Maybe the best solution would be to always use a root "WebAssist" folder and add subfolders under that. That seems to fix the clutter problem some have complained about, but I'm afraid there are too many drawbacks to actually allowing a user to specify their own directory when it comes to portability.
We will have to update it one extension at a time and in major releases since there will be a lot of testing involved, but I will certainly keep it in mind as we move forward.
