The two most prominent reasons seems to be:
- Further research
- Spares for usage of Izanagi/Izanami
As sheldon156 suggested, due to the immense powers of the Sharingan, there would of course be individuals (i.e. Danzo, Orochimaru) who desire to obtain it for themselves. Given the vast quantity we saw in Obito's lab, we can safely assume that he took all the eyes of those murdered in the Uchiha Clan Massacre (at least those who awakened their Sharingan), and though he did use them for his own purposes, the fact that they were locked in his lab means that very few, if any have access to it.