I have worked with both, though far more with SqlServer. In a large shop, especially one where many application architectural decisions arise from DB Architects, SQL Server offers more. Replication, SSIS, etc. But, those add a LOT of complexity, and in my experience have been the source of a good portion of operational outages.
But as a datastore for a software application, MySql does what you need and is straightforward, reliable, fast and simple.
Speaking strictly philosophically, you really want your application logic in your application code, not in complex SQL and constraint definitions. Go for the basics in your datastore, and put the time you save into the program itself.
