So whats your point? Justifying a flaw by mentioning another stupid "feature" is not the smartest thing.
And as far as I understand it real world FT shooting is somewhat of an untrainable skill.
Just that using "realism" as a determining factor of how the game should work is also, in your fine words, not the smartest thing - imagine the uproar if the games economy were tilted toward the top teams and leagues as it is in real life.
As a game concept, FT is being treated like any other skill - if you want it to get better, you train it. If not, you don't. Where there should be improvement is that the curve should be such that low skills should occasionally hit FTs and going up from one to three shouldn't represent such a major improvement. But there's no reason at all to say that it should be trained along with JS or the like, especially since it's the easiest skill already to train.