What makes you say "Advanced settings" dialogs mean poorly thought out UI? I think it's a very good way to tell novice users, "don't open this panel if you don't know what you are doing". And if they still do it and something wrong happens, they'd immediately know the reason.
User has trouble with software. User says that software is "too hard to use". A usability/interaction team are tasked with making the software "easier to use" and set off to find "confusing and infrequently used" features they can kill off.
Obviously anything on the 'Advanced...' dialog makes an easy target.