The usual reason is fragmented data in the data cache buffer where temporary data is stored. Over time it becomes fragmented and when you go to store some temporary data it has to reorganize the space to permit the storage. That reorganization takes CPU cycles and slows you down.
If you did a major system update *Jelly Bean to Kit Kat as an example) it is strongly recommended that you do a Factory Data Reset after the update. If it arrived with Kit Kat already installed then the Factory Data Reset should not be needed.
The Factory Data Reset will remove any apps you added and any customizations you defined and your contacts list. It should not be done casually. It should be done after every major system upgrade.
As you run the cache buffer fills with temporary data. It fills and fills and when some contiguous space is needed it is compressed to make space. Over time it can get fragmented. This is ONLY temporary data the is created by apps running on your phone.
The slowdown occurs when the system defragments the space to permit some new temporary file to be stored.
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