There would be some hurdles in Unity... especially if you're not a coder.. I think you'll run into issues with applying the movement methods with perspectives in unity... Among other things... But it would probably be easier in unity as it is already 3D capable...
You mentioned having variables to store position information....
I am not quite sure I understand what you're trying to do but I have thought about how to do a Fez-like game in C2 and I feel it is most easily done by using an array to store all positional information... Basically, having the whole game be handled in an array and the visual elements merely being interpretations of the happenings within the array.. Usually, when this is done, you end up with choppy/tile-based movement, but you can overcome this by using a gigantic array and oversizing your action sprite as well as implementing some clever algorithms to handle things like acceleration...