-snip-
He planned it all out, sorta like a play. He knew what He was going to change the rules as different circumstances arose. God according to the bible is all knowing of all events in the past, present, and future. Just because He changes the law according to his relation to humans does not mean he is "flawed" in your man made academic standards.
Also, yes, we are his "puppets" as you would state it, but He isn't pulling hard on the strings right now.