I do not believe A level results represent an accurate portrayal of one's ability at the end of their course, which is of course what they should be. The modular nature of them plays a large part in this, but there are other factors such as the fact that teaching is mostly geared towards passing an exam, rather than actually understanding a subject.
It is far, far too easy in subjects such as Maths to gain 100-odd percent without actually having a firm grasp of the subject. Compare an A Level Maths paper to a university Maths paper: it is not merely the content that is more advanced, but the actual style of question; they simply make you think a whole lot harder at degree level.
That said, many people do still find A levels very difficult. As a compromise I suppose they do work quite well. However if I were to change one part of them, I would place the exams at the end of the two year course (less stress in the middle, admittedly more at the end but that's life). I would also not have papers specifically targeted at certain areas of the subject; questions would come up about any area of the entire course. That way, people are forced to understand how everything they have learned links up with each other.