It is absurd to make invidious comparisons between specialist journals and multi-disciplinary general journals like Nature and NEJM. To compare journals you should stick to a particular category as is explained very carefully in the Guide to Journal Citation Reports.
Citation data and analysis should always be used in combination with other indicators when evaluating departments or individuals. For nation by nation comparisons, there is very little controversy about the use of citation indicators. Further, they have been used in the USA to evaluate 5,000 departments at the leading universities. Similar research assessment exercises are performed in the UK.