Linux filesystems do indeed need to be defragged -- about once every ten years.
the price we pay is that we can't fill our filesystems up past 95% full without things starting to break.
to see what is eating your CPU cycles, install htop.
then run it, and sort by CPU%:
sudo apt-get install htop
also: are you positive this decline in speed you are noticing isn't all in your head? i'm not calling you a liar, but i am sure i am not the only one here that has dreamed up a monster when in reality facing only thin air from time to time...