MySQL 5.6 service not going to stop
The issue might be happening due to innodb_max_dirty_pages_pct and innodb_log_buffer_size as before shutdown Innodb needs to flush all the dirty buffers. It depends on the buffer pool size that how much dirty buffers are there. 

You can check the link https://www.percona.com/blog/2010/09/02/how-long-innodb-shutdown-may-take for more detail.

In order to reduce the time, you can tune some mysql settings as mentioned in the blog https://www.percona.com/blog/2009/04/15/how-to-decrease-innodb-shutdown-times/