I'm totally spoiler-free in regard to the movie (Terminator 3: Rise of the Machines), but I'm hoping they address this.

If the Resistance ends up truly defeating Skynet in the present, John Connor should disappear.
I don't mean disappear from society, like the Connor's did when he was growing up, I mean he should actually be wiped out of existence. He should never happen.

Because if Skynet never gets built (or never obtains conciousness), then there will be no Human/Machine war. And John Connor will not become the leader of the Human Resistance in the Future, and therefore will not send his dad back in time to make sure he gets born.

I'm just sayin'.

(Let's see how much debate this entry causes. [wink])