I've always found that isomorphisms are more natural than homomorphism. Isomorphisms are motivated by the desire of defining when two structures are "structurally equal". But what is the motivation of "homomorphism"? In many presentations it seems that homomorphisms are motivated just as a stepping stone to the definition of "isomorphism".
But what is the real motivation of considering homomorphisms independently of isomorphisms? Why are people interested in studying these? Why do they help us reveal things about the structures we care about? What was historically the motivation?