They're a pain, but I think they need to stay for the simple fact that they cause coaches to have to make more decisions.
For example, do you want to recruit that stud player with the low GPA, knowing that you'll have to dedicate more of the practice minutes to Study Hall instead of individual practice, not to mention that his team IQ will improve slower? Or do you recruit the not-quite-as-good player who is a genius and can use more of his practice minutes towards individual skills and whose team IQ will improve at a much faster pace?
Like I said, Study Hall is a pain in the ***, but it also gives coaches more decisions to make, which I think is good for the game. We get enough spoon fed to us already as it is. Just a thought....