I agree with Christopher. Batman is an orphan, Spider-man is an orphan and lost his uncle Ben, Tony Stark's father died young in the cinematic version, James Bond is an orphan, Bourne has no family (that he remembers), Wolverine has no family, Captain America's family are presumably dead, Harry Potter is an orphan, the Starks lost their father and mother in GOT, Kirk's dad and Spock's mum died in ST'09.
The whole losing a parent thing seems to have become such a cliche of late. It might have been nice to keep Jonathan around in the MOS-verse.
But in this version, Jonathan isn't really a "mentor" figure. His role is more of the father of an "exceptional" child. He doesn't really have any answers for Clark--other than to keep his powers a secret.
What he does offer Clark is a symbol of humanity, and that part the movie did quite well. As a father, I often feel like I am stumbling along trying to find the right things to saw or the right answers to my kids questions and, in that sense, I really enjoyed this version of Jonathan Kent. What Jonathan does give Clark is an unconditional love and support--and that is really his role in this movie. I really loved the scene in the barn and at the truck, and I hope we get more flashbacks in future movies and see more of the father-son relationship.