CGH arrays are employed to detect chromosomal aberrations. Focussing on human genetic disorders, most of the major hospitals and diagnostic centres in the US have happily adapted microarrays. Thousands of samples are analysed on daily basis for a number of patients. Microarrays are allowing analysis , QC and sample preparation in large batches with cheaper costs.
Secondly, as mentioned above, researchers are comfortable with the analysis. Companies like Illumina and Agilent are providing free-of-cost workflow based software for microarray analysis which requires minimum knowledge of computers. On the other hand, most of the NGS based tools are open source and requires basic understanding of Linux. The transition is happening gradually but it will take time because the technology is different, the raw data is different and the down-stream analysis is also very much different.