I agree with Alias. It never occurred to me to compare Mortal Instruments with Harry Potter. Now Percy Jackson does compare with Harry Potter, but that is another thing. It seems to me that Mortal Instruments is primarily about human relationships - Jace and Clary, Valentine and his children, Alec and Jace, Simon and Clary, etc. Rowling is a lot more about power and politics, and of course, schooling.
Clare also moves her story along much faster than JK Rowling. (which is generally a good thing.)