Did YOU ever consider John a friend?
In the game itself Bruce definitely used John, used him a lot actually, but you could still do quite a bit to be friendly to him (I did pretty much all of it), but there was always a hint of deception there just because of the circumstances. On the other hand I as a player was constantly hoping for more friendly options, so I am very glad with the final John choice where you can tell him that he was actually a friend. I knew it was inevitable that he was going to turn, that was what made it heartbreaking, I wanted to help him and be nice to him.
That is why it's so sad that things ended up like this.
What about you? Did you or your Bruce consider him a friend? I imagine that most people who ended up with a villain did not, but if you did can you explain your reasoning?