One way of ensuring reasonable instrument flying skills is that instrument rating tests should be manually flown on raw data. This includes autothrottle and FD off. And not just one ILS, either.
There should be just enough use of automatics to ensure the candidate is reasonably proficient at button pushing. Currently in Australia at least, 90% of the instrument rating test in the simulator is use of full automatics. Automatics does nothing for basic instrument flying skills. The solution might be a compromise with the test being 50% on automatics and the other 50% of the test hand flown raw data.