During the HF route, Zouken wants to use both Illya and Sakura as Grails. His plan is to summon the Greater Grail to give birth to Avenger. But in Sakura there are the worms of Zouken. When Avenger assimilates Sakura, Zouken will take possession of his body through his worms.
Illya and Sakura are Lesser Grails with the same functions, so why does Zouken need both? In fact, one is enough. After Shirou and Kotomine saved Illya, Zouken proceeded to summon the Greater Grail using only Sakura.