I reckon the whole puppet master thing would be severely cool, and it sounds plausible. That and the Blue=evil thing would help explain why her “original power” is so powerless. Most of the time.
I still want to know how August knew Neal was Bae. Maybe he encountered the home office or Blue had something to do with it?
As to Regina being manipulated though, I don’t think the blame for her evilness should rest on Cora or even Rumple. No one forced or even encouraged her to murder Leopold, Graham, Kurt or those countless villagers. In fact rumple seemed quite disapproving of the village torching thing.