Perhaps an unintended consequence is that it creates more doubt and less confidence in making a judgement call.
They'd be far better off just doing away with it and giving the benefit of the doubt to defenders for penalties and attackers for offsides. Failing that, instead of getting involved in every little thing, let's take the best of other sports and see if they work for football. Let each captain have one challenge per half (a bit like cricket) and see if there is a reason to overturn the referee's devision (like rugby). If not, the decision stands. You could say the challenge can only come when the ball is out of play or if the game has stopped anyway.