using mySQL is quite simple...better than none. Most CMS Portals using mySQL as their database like mambo Opensource, DEV, phpnuke, and manymore.. but mySQL is not applicable for big organization as they need special DBMS to support their system like online banking systems. they rather using SQL manager in order to get better services..I think
either FTP or file manager..both of them have their advantage..but I think file manager is more user friendly than ftp..in certain cases using ftp is much better than using file manager on cpanel