The writers said that it was meant to wrap up the series and open up more possibilities. Since that never happened, a lot of people were left unsatisfied with what we got, but is that really the case? Here's what I thought the ending represents:
I think one of the underlying themes of the series is machines becoming more human, which is not only compelling but also makes sense once you think about it. As great at T1 and T2 were, they painted Skynet pretty black and white, since the human drama takes precedence over the sci-fi logic.If machines take over the world, then what? What does your refrigerator and PS4 wants once they've become legitimate citizens of the world? Do they even have "wants"?
Salvation and Geneshyte tried to solve this by giving some character to Skynet but it backfired horribly. Now they come off as Saturday morning cartoon villains with their mustache twirling justifications, and surprisingly- TSCC got this right, brilliantly right.
Look at the characterizations of the Uncle Bob T-800, Cameron and Catherine Weaver. They are all Skynet foot soldiers but had their perspectives changed due to prolonged human interaction. I believe Skynet itself is sentient and intents to create a world where only machines inhabit the planet, they're not evil but rather they see humans as flawed and a threat to their existence. Catherine Weaver was revealed to have broke off from Skynet, wanting to create a world where machines and humans would co-exist. Rather than rely on the biased messiah that is John Connor, she created John Henry- a machine nurtured with morals and ethics, to either bargain with Skynet or destroy it.
Which leads to John, Catherine, John Henry and Cameron's chip traveling into the future. Cameron clearly knew what was going on, and gave her chip to John Henry, with Weaver and Henry asking her "Will you join us?" indicates she was part of the plan all along. John Henry did as he was brought up to, and with John Connor tagging along that means his existence from 2007 to JD is erased.
So all this talk and what does the ending means? Why end with a cliffhanger by having John into the future? My interpretation is that Catherine saw John Connor as he is the ONLY human who empathize the machines, who has risked his life on several occasions to save Cameron- and this is what she wants Skynet to see, along with her child John Henry. The ending could turn out any way you imagine it, but to me Catherine Weaver had more than enough to convince Skynet of her viewpoint- a machine nurtured by human morals and a human nurtured by machines (Uncle Bob and Cameron) thus finally, ending the war.