Bale and McG eventually worked out all the kinks in the script. When Bale told McG he wanted the title role of John Conner re writes had to be done. The two had to figure out how to incorporate John Conner into more scenes with out making it seem like Bale was in the scene just because he is Bale. The change had to make sense. From what the two are now saying that has been accomplished.
"A lot of the work was integrating (Connor) into scenes ... and having that feel integral and sensible, as opposed to grafted on just because there was a star in the part" says screenwriter John Brancato.
At first the character of Marcus Wright had more screentime then John Connor. Since the Bale switch, the two share the same amount of screen time now.
McG was also asked about the original alternate ending, he goes on to say: "We had a jet-black ending. Connor dies, we’re in a room with all the people we care about. You take Connor’s likeness, you put it on the living machine of Marcus. He sits up, now looking like Christian Bale, takes a gun, kills Kate, kills Kyle, kills Star, kills everybody, eyes flare red, [snaps] the end" states McG.
And finally will the topless Moon Bloodgood scene make it to the DVD/Blu Ray release? McG states maybe. Not to distract from the sci fi feel of the film the Moon Bloodgood scene was cut, McG goes on to say "it felt more like a gratuitous moment of a girl taking her top off in an action picture, and I didn’t want that to convolute the story or the characters."