When I first finished FF7, I was so confused that I thought maybe Cloud was a failed clone of the "real" Cloud (which explained why Tifa wasn't sure if he was himself), and that he was a puppet of Sephiroth.

Or something. I don't know quite how I got that impression, since it meant that I failed to comprehend Tifa's mindmeld sequence, but I played the game very sporadically over a long period of time.