I don't know about final fantasy, never watched it never will.
However I can explain the matrix to you.
In that quote, it's not actually Agent Smith speaking, it's the oracle speaking THROUGH agent smith. The reason I say this is that Agent Smith never called Neo anything other than Mr.Andersen did he?
This makes neo understand that the only way to beat smith is to let smith take control.
I remember I read an article on this before. Link is this