A perfect example, in my case, would be the splitting up of the controller files since I first created my site. If I had an include statement in each controller, I would have had to change the include statements in all of my controllers to reflect the new locations of those classes. Since I did not have the include statements in the first place, I did not need to change anything to reflect the new locations of the classes.
For some people, this isn't a big deal. Personally, I have a lot of controllers, and I don't want to have to change every file which extends Admin_Controller or Front_Controller just because the file containing that class moves to a new location or the name of the file changes for some reason.