Like you'll really fly an NDB approach with a plane load of people...
It is precisely this misunderstanding that, in part, causes the problems. There are many places on Europe, served by scheduled aircraft, that do not have anything other than an NDB (and perhaps, if you're lucky, a DME) for IFR approaches and so the pilot doesn't have a choice. The reason that the JAA IR includes the "the most inaccurate and the most dangerous non precision approach" is because pilots do have to fly it with an aircraft full of passengers, maybe followed by a circle to land!
However, the point is well made - there is nothing whatever wrong or inferior about FAA training, it is at least as good as EU training but designed to serve a different need. One of the things one might reasonably expect an instructor to do is to pass on his (or her) experience to the student. If the instructor does not have any relevant experience, the student is at an immediate disadvantage.
First time pass rates are a notoriously crude and, generally, misleading measure of a school's quality and I would not normally advise placing any reliance on them. But, when one hears of an otherwise well-regarded, US-based JAA IR course provider who has not yet managed to produce a student who can achieve a first-time pass, one has to wonder. Perhaps, in this case, this is a question worth asking before parting with any money.