They are two different types of TEs. Graham, like Hernandez, is more in the Tony Gonzalez mold of a WR in a TE body. That is why he runs longer routes.
The thing is. Even with Graham running deeper routes, Gronk has more yards per catch (15.2 vs. 13.5) and more catches for more than 20 yards (19 vs. 17), and more catches for more than 40 yards (3 vs. 2). And the key stat is that Gronk has more TDs (15 vs. 9).
I guess that I don't watch enough Saints game to know how much YAC Graham gets, but that is one of the things that makes Gronk easily the best TE in the game and it really isn't debatable. Gronk does run shorter routes than Graham, but he has more yards per carry and more big plays because they guy is impossible to bring down.
I look at Gronk and he is a match up nightmare that is unique to the NFL. There isn't a receiver harder to bring down after he catches the ball than Gronk. We have seen two and even three guys trying to tackle him at once and see them basically bounce of him.