I don't pretend to know the details of why OS X doesn't take care of these things itself. What I do know is that repairing permissions and cleaning up OS X system cache files can both eliminate application problems as well as keep performance up to peak.
You can repair permissions manually by launching Disk Utility, selecting your drive volume, and telling it to 'Repair Permissions'. When file access permissions get out of whack (don't ask my why they do, but they do and this is regular maintenance you should do with Disk Utility), applications can run slower, have problems performing certain operations, or even unexpectedly quit during use. Repairing the permissions brings file access rights back into proper line so the resources are available correctly as various applications make use of file resources.
Cleaning up your OS X Cache requires some 3rd party help - short of reinstalling your OS from scratch. When I recently installed 10.4.8 Update, boy did my system come to a screeching halt. Everything was running, but window redraws were agonizingly slow and it made every operation requiring a window move or opening very painful. While I only first noticed this after doing the update, this sort of 'phenomenon' can occur independently just from normal use too and repairing the permissions doesn't take care of an excess or corrupted OS cache file issue.
For owners of Macs with a PowerPC processor I highly recommend AppleJack - which we've covered in a prior quicktip. Once you install this utility, you boot into single user mode which is perfect for the system maintenance it does. What's also nice is that with a single command it will automatically run through the five maintenance options it supports, including the cache clean up and permissions repair in one swoop. I recommend this application be installed too just for the OS repair help.... More often than not, should you have some flukey OS X flake out where it won't boot - AppleJack has proven a real saver there too.
Unfortunately, Applejack is not an option for the Intel Macs. There is apparently some bug that prevents command line execution of the needed tasks where the Intel Mac is booted to Single User mode - and that's something Apple has to fix before AppleJack will come out for Intel Macs.
But, another option that is available for Intel Macs and PowerPC Macs alike is Cocktail. This application runs under OS X via the finder just like any application and allows the manual running of various maintenance options (including the important cache cleaning and permissions repair) as well automated scheduling of this maintenance as well. Unlike AppleJack, this application is ShareWare - so it is not free, but they'll let you use it ten times before making you buy. For those that need it or see a the uses beyond that which AppleJack provides, I personally find Cocktail well worth $14.95 you'll pay to own it clear.
And that's that. In my opinion this kind maintenance shouldn't be needed to begin with, but - since it is, those applications noted above make it really easy and the benefits are definitely there for doing so.