The GOP plan does away with the student tax deduction, not to simplify matters, but to punish intellectualism since they're not voting GOP anyway. You can tell, because if they actually wanted to help people, there would have to have been long discussions with heads of universities to come up with a plan to not harm grad students. Obviously, that didn't happen.
I'm not sure universities are to blame for fudging things to, say, get better tax treatment. That's just how the laws are set up. The new plan will do nothing but harm universities, their teachers, and their students. Everyone is still completely correct to blame the GOP for screwing them in this instance.