At a guess, there's little or no oversight of the JLPT system, which is probably run by semi-retired bureaucrats as their little empire, and no attempt to gain feedback from examinees so that they might improve their service, so therefore little impetus to change the system, which has probably remained largely unaltered since the exam first came into existence despite technological advances. I imagine the one big change (the introduction of the level betwen the old 2kyuu and 3 kyuu) was at least parly motivated by the prospect of increased revenue.
Do they still have that ridiculous yellow card and red card system for misdemeanours?