As a simple example, back in the earlier days, Wordpress was mostly a collection of a many, many functions. As it has matured, it's become more class based and slightly less functions. Perhaps more importantly, many of the functions now have quite good phpdocs so you can simply grep the code to figure out what you want to do. Also, as WP has matured, it's added a lot more hooks and actions for various things you might want to do, so it's become less and less necessary to hack core.

It is still relatively brutish code, but damnit if it doesn't work pretty well.