You make that sound as if you think that's a bad thing!
Apple has never produced a perfect operating system, and that being the case, a little tweakage is sometimes necessary.
I believe that reverse-engineering applications and injecting custom code into them to modify their behaviour is a very bad (even though quite fun) thing. Don't like a stock option? Why not develop your own app that is better? This way you are in total control over the code and avoid the risks of introducing subtle bugs or vulnerabilities into the system or potentially needing a complex update every time the OS is refreshed.
Of course, as you say, OS X is not perfect. At this time, Apple is pursuing a very interesting path to address these issue, in form of system-wide extensions. The current APIs for creating plugins and communicating between processes in OS X are quite advanced, e.g. you can even share GPU memory between applications. Common plugin interface allows OS X to solve the issue of extendability in a safe, controlled, user-friendly way. For instance, I can use the advanced photo-editing capabilities of Pixelmator in iPhoto. The extensions are still very young of course and the API leaves much to be desired. However, the potential utility is enormous! Frankly, I am surprised that extensions, which I consider to be probably the most advanced and exiting development in OS X in the recent years, don't get more attention in the discussions.