Sure. Allowing to set ranges yourself rather than infinite scrolling that makes it impossible to go back to number X. A setting to always show little icons instead of only when the mouse hovers over it. Settings to organize lots of data the way you want. Settings to let a single mouse click on a bookmark star put it in the place you want rather than some place where you don't want it. Settings to always expand all content in a thread rather than showing things collapsed first so that you need to open each individually. Settings to put the refresh button next to the forward and back button. A setting to have multiple rows of taskbars in your favorite Linux desktop env. Settings to fix anything that's annoying and designed for less knowledgeable users or users with small screens basically.
One example that sums up most: Twitter. I just want to see/display the feed, not have the UI decide which ones to deem 'important'. I'd like for the app to allow the power of CSS to let me choose a layout as opposed to just picking one that doesn't really work for me.
The overall problem is that what UI designers think 'a more suitable UI' is, probably won't be for many users. Think of it like the open-office plan. It's horrible for employees, most people absolutely hate it, it lowers productivity, and yet corporations have people on staff who are implementing it as fast as they possibly can because it's more "suitable".