The "father" line is, in fact, one of the (again, few) problems I have with the Final Cut. I do, however, like Roy apologizing to J.F. - I think it fits well with the emotional state we see him in during the next shot, in the elevator.
I also still have a problem with the fundamental concept behind the unicorn scene, but that's because I refuse to see Deckard as a replicant. I feel like that undermines the whole film.