Chud's got a really good article on what went wrong with Terminator: Salvation, and it turns out that most of our speculation is correct:
* It was intended to be a story about Marcus
* John Connor was barely in the movie
* Connor dies, and is replaced by Marcus
The article goes on to give a lot more detail about the original script:
>>With John Connor relegated to the shadows for most of the film, the original Terminator Salvation focused more on the relationship between Kyle and Marcus. Star was always there, and was essentially always just as useless, but without the constant cutaways to pointless Connor scenes the film was able to delve more into Kyle/Marcus. The script spent time examining what it was like living in a post-apocalyptic world, and was more definitively R-rated. At the gas station Marcus saves Kyle and Star from a group of cannibals, throwing one of them into an open fire (intended as a callback to the biker on the stove in T2.<<
Rather than praise the original draft, however, Chud goes on to say:
>>It's important to note that the original script by extraordinary hacks Brancato and Ferris - the guys who wrote The Net, Catwoman and Terminator 3: Rise of the Machines - is not some discarded gem. It's got plenty of problems of its own).<<
Holy Crap! They let the idiots who wrote T3 have another crack at it? I did not realize that. In any event, Connor has gotten so freaked out by time-traveling assasins that he never ventures out of his hidey hole, and addresses the troops by radio.
>>In the original script the title Terminator Salvation actually meant something. Watching the finished film it's hard to figure out why it has that name - is it because Marcus saves Connor's life in the last minute? In the original script Serena has a bigger role than a quick cameo, and she explains the salvation element.
Marcus comes to Skynet City and finds... a seaside resort populated with humans. He sees Terminator landscapers! It turns out that Skynet hasn't been trying to wipe out humanity. It's been trying to save us.
This is perhaps the most bizarre idea in the whole script, and the one that most obviously doesn't work. It seems as though Brancato and Ferris thought people liked the Matrix sequels, as this all feels like it could be in those films. See, Serena heads Project ANGEL, which is making Hybrids (ie, Cyborgs). The reason? Skynet did a calculation and realized that humanity was going to be extinct in 200 years; the machines decided to save a few by turning them into Hybrids and wipe the rest out. It makes no sense, and is the kind of thing that makes you wonder if these guys ever even watched the previous Terminator films.<<
Ha! R2 will love that! His preacher was suggesting merging the Terminator and Matrix universes anyway, suggesting The Matrix was in a future where the machines won. Kyle dies, sort of, and John Connor is mortally wounded:
>>John and Kate beg Marcus to take up the mantle of John Connor - since no one has really seen him anybody can be him. The legend is bigger than the man, they insist.
Marcus agrees, and John Connor's face is grafted onto Marcus (this, it turns out, is the source of Connor's scars. You would think they would have cut off his face from the back of the head, under the hair, but I guess not), despite the fact that nobody really knows what Connor looks like anyway. But it's done, and Connor dies and Marcus now must step up and lead the Resistance into the future.<<
Well, it's a clever idea I wouldn't have seen coming, I'll give 'em that, but I'm not sure how it would have played on the big screen. I'm not sure it would have worked out any better than the mediocre movie we got. In any event, the article is a completely fascinating take on the deterioration of an iconic franchise and it's well worth reading. Check it out here: http://chud.com/articles/articles/19577/1/EXCLUSIVE-WHAT-WENT-WRONG-WITH...
Special thanks to Church for pointing this out to me!