Yes, I would say Winstep Preferences is a bit the Achilles heel of Xtreme, for two main reasons: first the controls in it emulate those of NeXTSTEP (this was a conscious decision at the time because back in 1998, when NextSTART was first released, the NeXT look was the thing we
all aimed for) and second, Winstep applications are so powerful and so full of features that all the settings are kind of crammed together (a bit like the cockpit of a 747

).
Over time a huge effort was made to organize things better and provide an easy 'out of the box' experience for the first time user. This was accomplished mainly through the use of well thought out defaults and extensive use of context menus. For 90% of users, what is available through the context menus is amply adequate.
It's only when you really go for the extra power provided by Winstep Xtreme that you must master Winstep Preferences. This is where the learning curve gets a bit more steep, because, unless you take the time to read the User Guide, not all settings are self explanatory, and not all of them will be where you expect them to be. It can be a bit confusing at first, although a bit of perseverance will result in a HUGE reward at the end.
Winstep applications can basically do anything you can think of in their field of action, you just have to figure out how. There is a LOT of functionality crammed in there, because Winstep's focus has always been on functionality rather than eye candy.
Let me give an example: you can make as many different menus as you want, you can attach specific menus to specific applications, you can have menus popping up by bumping different screen edges or different spots on your desktop, you can have horizontal menus that turn vertical with a single click (and vice-versa), you can have menus rolled up that unroll when moused over, you can re-order tasks in the tasklist, you can have your quick launch buttons displaying menus or running internal commands, you can have a desktop where NOTHING is visible until you start bumping screen edges or the opposite, where everything is visible at the same time, you can have your tasklist or systray detached from the startbar sitting individually on the desktop (heck, you can even turn off the startbar), you can make Winstep widgets move into the startbar with a single mouse click, every item on menus, shelves, docks, have REAL context menus (i.e.; with all the options provided by Explorer) and can be run with a keyboard hotkey, image and video files can be displayed as thumbnails, you can drag ANY object to and from Winstep applications (and that includes virtual shell items like the Control Panel items, etc...) and etc, etc, etc... I could go on and on, but everybody would have fallen asleep by the time I finished (and this post would be a mile long).
The possibilities are endless and attention to detail is what makes Winstep applications special. As Nelson Mandela once said, "it's enough to make a grown man weep with joy"