This is one thing I really liked about Head Coach, the overall rating for a player was based on what your philosophies were. For example, if you ran a 3-4 defense, you would set the philosophy to favor a good 3-4 DE, which would make power/size much more valuable than speed/finesse.
On the current system, it's all the same. Robert Mathis and Ty Warren would both get high 80's ratings at defensive end. But in a 3-4, Mathis would be a terrible DE because of his speed and lack of size. Meanwhile, Warren would suffer a bit as a 4-3 because he's a big powerful end, who would be more suited as a DT in that scheme.