This one would cause many logistical issues, but in a perfect HD world I'd like to have additional ratings:
Instead of ATH alone, split it into strength and agility.
Instead of PE alone, split it into 3 PE, mid-range PE and finishing ability (getting to the rim and MAKING the layup in traffic).
Split DEF into perimeter and low-post versions.
Add "headiness". This would be independent of IQ, which is knowledge of a system, and comes with experience. Low headiness would increase chances of turnovers and missed defensive assignments (dumb plays), while high would help create turnovers and assists and team rebounds. Would also significantly override low IQ for young players, which would allow a Mike Conley type player. In HD, a Conley is as inept at running an offense as anyone else, if he has F (or even C) in the offense being run. But give him 98 HE, and he's able to thrive.
Split REB into offensive and defensive, which are very different skills.