"The player doesn't just play any Big Daddy, he plays a prototype Big Daddy — the very first one that was successfully created," BioShock 2 exec producer Alyssa Finley told website CVG. And as a prototype, this Big Daddy is quicker and more agile than the standard Daddy. The prototype also has the ability to switch weapons and use plasmids. However! It is not as powerful as the other Big Daddies.
"Another thing that is special about the prototype Big Daddy is that he has somehow regained his free will which is a very important distinction," said Finley. That free will allows players to grapple with the moral choices and interact with Little Sisters. "You aren't a stranger to them, you are Mr. Bubbles and they look to you for protection," Finley added. "What you do with that trust is your choice as the player."
Questions that remain include how the player became the first Big Daddy and why did someone think a quicker, more agile Big Daddy should only remain a prototype?
BioShock 2 Interview [BioShock 2]