I doubt that Rumple is Regina's father. If The Miller's Daughter reveals anything resembling the orginal tale, then I predict we'll find that Rumple made a bargain with a poor but ambitious Cora to enable her to marry Prince Henry in exchange for their daughter (who he knew could one day become the Evil Queen he needed). Perhaps the twist will be that he taught Cora magic in order to help her spin straw into gold, or perhaps she came to him later wanting magic.
As a side note, if she did admit that they were living in poverty (Stable Boy), that's a bit odd since she clearly learned magic from Rumple and the man is never in need of material goods.
I also think her knowing magic will shows us a wizard's duel reminiscent of Merlin and Madam Mim. That's a very ancient magus match trope, btw.
I guess (and hope) you've hit the nail on the head here, because that's definitely something that will be very fascinating to watch.