SQL Server 2016 high idle CPU and queries extremly slow
Since your CPU utilization is low (and you have a great CPU set), I would check for memory pressure first. With SQL Express 2016 you are limited to 1410 MB of memory, but your VM only has 2GB. Give your VM 1GB more of memory and see if that helps. You can also check your SQL Server log if it is paging memory to file.

If that does not work, try setting the database setting LEGACY_CARDINALITY_ESTIMATION to ON. Reference: Using DB Compatibility Level 130 with Old CE in SQL Server 2016. We ran into this with some of our upgrades; results will vary with each database.