The training court facility has turned it into a formality that any trainee can eventually reach 15+ and even 20+ FT rating, numbers you would seldom see in the past. Whilst I have a hunch that free throw percentages have been tuned down in the GE to compensate, that still might not be enough in the top leagues, as more players who were drafted after the training court addition reach their prime.
My proposal would be to place a cap on Free Throw rating, so that it cannot exceed a players Jump Shot* rating at any given time. Most well trained players would still be good shooters, but short of some highly inefficient builds salary wise, no-one would be shooting 100%, and the overall percentages would be more well balanced for top flight play.
The only drawback is that this might make the training court a bit under-powered for it's weekly cost, so I also propose a review of the weekly costs of arena facilities in general (I haven't seen a reason to invest in anything other than the Gym and Training Court as it stands).
*Alternatively, whichever skill is higher out of Jump Shot OR Jump Range.