I don´t think it so bad that you can´t choose the heir, I can´t recall to have ever done it in RTW. What really bugs me is the mess that results if your heir has no children of age when he becomes king. Then the sucession just seems to run amok through the family tree.
Not that it matters that much for gameplay purposes, it just looks extremely untidy and weird.
The only way to bring the sucession back in line is to deliberately kill off the out-of-line heir.