I completely agree with all the above. The JAR ATPL exam system, when I did it a while back, did not prepare me well for my IR training or for my airline career. So much time wasted on pointless stuff and more time in IR detail briefings covering stuff that should have been included in the ATPL theory.
There was far to much reliance on memory, and practising of feedback questions, and not much testing of problem solving ability or on understanding of the concepts. It does sound like at least in the US, some of this is covered in the oral exam before a skills test but when I did mine, it was not the case in the UK.
It's a bit like the "Lift theories" thread elsewhere on PPRune. We were taught stuff in order to pass the test. It didn't matter if it was right or wrong and I remember many an instructor getting quite defensive if I asked a question that was even slightly deeper than those on the syllabus. This is all in stark contrast to my time in uni where debates and questioning were encouraged and that proper understanding was expected and tested for.
I cannot criticise the ground school organisation for the job they did in getting me through the exams. They did what was necessary and were very good at it. It's the system that's at fault and this ground school had an excellent strategy for getting the results I needed.
Now, remind me the titles and numbers of those 18 annexes. I'm gonna need that info for tomorrows duty...