As Will said, Ben was just well-written. He was Peter, and yet he wasn't Peter. His unique experiences led him to have a slightly different personality, make different choices, and he even started using his head long before Slott's revitalization of Peter's scientific nature. Unlike Peter who was burdened by Spidey, Ben seemed to enjoy it. Yes, there was drama, yes there were setbacks, yes there was girl trouble and his being misunderstood, but through it all Ben just seemed to be more optimistic than Peter had been in a very long time.
Ben was never intended to be a throwaway character, and a lot of love and care went into his creation. And, not only did he win over fans, he won over many of the creators. Say what you will about the Clone Saga as a whole, in the end we got many great elements out of it. And one of them is Ben.