I have broken my promise to stop writing about this. Sorry, but I had to correct my mistake. I ran three micro-benchmarks: get by primary key, get by secondary key and update by primary key. MySQL had a higher peak QPS for all of them. Alas, the results for get by primary key were skewed because pymongo, the Python driver for MongoDB, uses more CPU than MySQLdb, the Python driver for MySQL. The client host was saturated during the test and this limited peak QPS to 80,000 for MongoDB versus 110,000 for MySQL.
I repeated one test using two 16-core client hosts with 40 processes per host. For that test the peak QPS on MongoDB improved to 155,000 while the peak for MySQL remained at 110,000. That is an impressive result. The results for get by secondary key and update by primary key are still valid as the server host saturated on those tests.
Now I must consider rewriting the test harness in Java, C or C++ or I could add MongoDB support to sysbench. I prefer Python. In addition to under-reporting MongoDB peak performance it also under-reports MySQL performance. I am able to get 180,000 peak QPS using sysbench on one 16-core client host and mysqld on another versus 110,000 using the Python equivalent.