I entertained the idea of Cutter being CJ, but for the reasons you listed, I think it would a bit implausible. I know that it's been a minute since CJ was last seen, but the last time he was in town he was about eleven or twelve years old. I remember when Sarah was back in town for all those months as 'Flash' and no one knew who she was, and I thought that was silly. I could understand if CJ and Sarah were hardly known by anyone, but they used to live at Llanfair with Viki and the rest of them. Peoples faces don't change that much from childhood.
That's my rant about Cutter being CJ.
As far as Aubrey is concerned, I don't have much of a problem with it if she turns out to be Katrina Karr's daughter. I just wish, if she's the daughter Karen and Marco stole and gave to Jenny, that the show would have used her original name.