The built-in MySQL schemas have problems - mostly that schema changes can take hours or days on large tables. As a result of this you need to build a system that doesn't require schema changes at the MySQL level. This doesn't mean you can't use schemas at a higher level though.

There are two ways to build on top of MySQL - you can either make a flexible schemaless structure with objects and properties and associations between them, which is what Facebook advocates for, or you can make a flexible virtual schema that has column names, types, and arbitrary indexes. I'm in favor of the latter.