OK I had this same problem and solved as follows:
MySql.Data.MySqlClient.MySqlConnection msc=new MySql.Data.MySqlClient.MySqlConnection(myConnectionstring);
System.Data.Entity.DbContext tE1 = new System.Data.Entity.DbContext(msc, false);
Then use tE1 to work with your data....tE1 can also be an EF6 context with all your typed datasets and so on...........
The important thing seems to be to override the default DbContext connection with a MySQL specific connection. It is a mistake to use an MySQL connection string with the default context connection, even though this "mistake" seems to work fine for most purposes.
Jeltz