Installing OS is painful, you need to re-install all the software and configure them to the way you want. We don’t want to wast time in doing this. To prevent doing this dirty job, we perform an upgrade install instead of clean install. We all have experience of upgrading Windows sucks, same as OS X. All the issues you have in old system will be remained, and sometimes new issues will be introduced in the process of upgrading. The system will be slower compare to clean install one.