How else could T3 end? If john had defeated skynet then the terminator would never had existed in the first place to go back in time and try and kill him. That future is inevitable because the future has already happened. It's like in the time machine. He goes back to save her over and over again and she dies. He built the time machine to save her but if he does manage to save her then there is something we like to call a "Paradox". why would he have built the time machine?
I will try and simplify this for you. Lets say you go back in time and accidentally kill your father before you were born, lets say he is 8 years old and something you do contributes to his death. How could you have been born to build the machine? Paradox.
The terminator franchise is just that. a paradox. you cannot change the future because events from that future helped mold and change what you did.
it can be confusing
This might strike you as bizarre, but I understand the concept of a paradox fully. Bizarrely enough, for about ten years, the Terminator franchise was left with a paradox of sorts as its ending, and no one complained, because it was the conceit of the movie. It was, as the poster below you unintentionally may have supported, the "plot hole" that one was willing to allow for the movie to work.
Likewise, in Back to the Future, when Marty arrives in future 1985, he has been living a "better" life, and thus would likely have had differing circumstances, and been a different person who may have not altered the past in the same manner that the Marty we had been watching had.
We let that go. Dismissing an ending that erases the good work of the *point* of a previous movie in the series because it might cause a plot hole that every single movie in the history of time travel movies manages to possess is foolish.
The original Terminator film is *built* on a paradox: Kyle Reese (from the apocolyptic future) is John Connor's father. Without John Connor, Kyle Reese would not have volunteered to go back in time to save John Connor, because he wouldn't have needed to. Thus, in the "first" time line, John Connor never existed. Considering that is the conceit of the first movie in the franchise, it is, frankly, silly to say that Terminator 3, over ten years later, needed to be made the exact way it was made because of the possibility of a paradox.
What I'm getting at is not really the "nitty gritty" necessarily. I'm not trying to "over analyze" the series (well, maybe a bit). I'm arguing about the merits of the *theme* of a film, using scenes from that film. Whether we like it or not, T2 was a fantastic action movie not just because of the 'splosions (though that helps) but because of a very well-told plot with a solid message backing it up. What upsets me about T3 is that it, in a way, undoes that good work in T2, not some silly minor details about what SkyNET *is*- that's just for a bit of lively discussion.