Just saw this interesting quote from Brian Austin Green where he talks about what happened at the end (making this the OFFICIAL explanation for people who were doubtful):
Green elaborates, "You have this episode where John Connor travels to a future where John Connor never existed. I don't know if people completely get it because we work on a string theory, which we've dealt with during the season. We dealt with that with Jessie, in the future that she came from there was Charles Fisher, who tortured everyone. In the future I came from, he never existed. I don't remember him. We were still together within these parallel futures but they were still different and they still had their own paths. This is the same concept. For John Connor to travel to a future where he never existed, where Kyle Reese never left, where Derek and Kyle are still fighting side by side, where Allison (the human Cameron was based on) is still very much present, what becomes of John? What better situation for somebody to grow up in and become the future leader than that? Than to be fighting in what he's been trying to prevent? Not just being the top dog, being listened to for everything, but having to actually listen and follow."
http://tv.ign.com/articles/973/973668p1.html
so (atleast part of season 3) will have John fight the machines and defeat SKYnet (and grow up, so, mid season actor swap?) capture the time machine, and go back, so he can fight the machines again?
I think the plotline would only work if the Kyle Reese-led resistance is in some way ineffective. What would be the point of traveling back in time if he has nothing unique to offer the resistance (as leader)?