I'll try to be as spoiler free as I can with this, but if my predictions turn out to be true...then I guess that would technically make them spoilers too ;)
So I've been thinking this for a while now, but what "Ms, Weaver" said to Ellison in the elevator in episode 20 makes me almost certain of it now. Through out the series they have hinted and alluded that perhaps there are some computers/robots/ai that wish they could find a way to live in peace with the humans in the future. I believe Weaver/T1001 was sent back to create a new AI that would be able to stop SkyNet from starting the war. The only way to beat a malevolent AI, is to make a benevolent one with empathy and compassion that will defend us. This is what I think John Henry is meant to be. This is why they have now revealed his "evil brother." That AI, which is apparently already killing people in full force and mighty powerful, is the one that will become SkyNet. John Henry's purpose is to prevent SkyNet from ever setting off Judgement Day. This would also explain why Weaver has shown no interest in looking for the Connors.
Unfortunately, what will probably happen is that Sarah, John and/or Cameron will kill John Henry by the end of the season, only to learn afterward he was meant to be their protector.
If I'm right, I'll be extremely happy with this narrative-wise. It has always bothered me that people just assume a SkyNet/Matrix like future is inevitable if we create true AI one day...but no one ever thinks about how to prevent it, offering a solution rather than just an empty warning. iRobot (the recent movie, not neccessarily the book as I've yet to read it) kind of hinted at this before, but I think it needs to be explored more. Why do humans not kill all the "lesser" life forms below us? Sure we need food, and we have the forethought to know we couldn't live without some of them...but the real core reason is empathy. It's built into our dna. When we empathise with things, when we humanize things that arent human, we give them some sort of importance. We value their life. So if we're going to create real AI someday, even if it's hundreds of years from now...empathy must be a fundamental feature of that program. And perhaps the writers of TSCC have realized this too?
Update 2009-04-11 (Spoiler Alert!):
Ha! I was totally right about Weaver and John Henry....and I'm very glad to see they didn't kill him off like I was expecting. I also just realized that Weaver is the T1000 that was in "the box" on Jesse's sub. Now where they've taken it...wow, I have no idea what's next. It's looking like we get to see a future without John Connor. I'm loving this show right now, I really hope Fox doesn't kill it off