The wizards are handy..i rarely use them but only started using them in the new databridge for a quick turnaround on a project..usually i just use the server behaviour panels.
i guess with the wizards being complex, this could be a benefit for some people if they require certain things that a simple wizard just cant allow them to do.
with regard to the file structure, I find that it creates everything neatly into one directory, consolidating everything together which is perfect :) I havent experienced it creating duplicate directories that mimic the older way of how the webassist products split their files.
and as for ADDT, I hated the way it created its directory structure. its a fair time ago now, but I think it was the same before Adobe purchased the company that produced them. I hated them since they always created unwanted files that I wasnt using for the product. at least Webassist only creates the files that are needed for a particular behaviour (such as encrypted passwords, it will only create the encryption file that you requested.
It is interesting though to learn how some users are having problems, when others like myself dont have any problems with the software working. I do wonder why as I dont have anything special on my computer.