The Skynet from the 1st movie isn't the same as in the 2nd , the 3rd or the 4th. Each is a new iteration of an inevitable evolution. Sometimes more advanced, sometimes less.
Time line 0 - Skynet evolves in mainframes, is attacked by humans, retaliates and WINS the war. Humanity is reduced to research animals. Ongoing research leads Skynet to investigate time travel, but none of its machines can go thru. SO it plucks a test subject out of the herd (Kyle Reese), stuffs him into the machine and turns it on to see what happens.
Time Line 1 - Kyle Reese, machine concentration camp survivor, is sent back in time and meets Sarah Connor. He's probably raving mad, malnourished, maybe even injured. Sarah nurses him back to health, learns his story, falls in love, and conceives John, their son. Kyle doesn't survive his injuries. Sarah raises John, trains him, prepares him. Skynet evolves in mainframes, is attacked by humans, retaliates and LOSES the war. But, time travel research is a little farther along in this iteration, so it sends back Arnie to kill Sarah Connor.
Time Line 2 - Kyle Reese, human freedom fighter, is sent back in time to protect Sarah Connor from Arnie. Sarah learns his story, falls in love, and conceives John, their son. Kyle and Sarah destroy Arnie. Sarah raises John, trains him, prepares him. Skynet evolves in the internet (due to pieces of Arnie), is attacked by humans, retaliates and LOSES the war. But, time travel research and terminator R&D (due to pieces of Arnie) are farther along in this iteration, so it sends back the 1st Liquid Metal Terminator to kill John Connor as a small boy.
Time Line 3 - Kyle Reese, human freedom fighter, is sent back in time to protect Sarah Connor from Arnie. Sarah learns his story, falls in love, and conceives John, their son. Kyle and Sarah destroy Arnie. Sarah raises John, is training him, preparing him, but going a little nuts doing it. 1st Liquid Metal terminator is sent back to kill John Connor and 2nd Arnie is sent back to protect John. Both terminators and the original Arnie's parts are destroyed, and the primary researcher is killed. Its too late, the info wants to be free. Skynet evolves in the internet, is attacked by humans, retaliates and LOSES the war. But, time travel research and terminator research are farther along in this iteration (but Liquid metal research isn't as advanced, since these models need an exoskeleton to function +'s are on board weapons, -'s are can't mimic non-human shapes). Skynet knows from research and prisoner interrogation that it has made at least two attempts to kill Sarah and John Connor in the past, both of which failed. So it sends back the 3rd Terminator to kill John Connor's most effective fighters.
Time Line 4 - John Connor is a nobody. Hiding. No records, no life. Mom is dead from Cancer. But Judgement day didn't happen when he was told it would. Maybe it never will. 3rd terminator is sent back to kill Johns future commanders. 3rd Arnie is sent back by Johns Wife, after his death by assassination, to protect him. 3rd terminator is destroyed, John, his future wife and most of his commanders survive. Judgement day happens.
Time Line 5 - Before Sarah Connor Dies of cancer, Future John sends back "Alison?" terminator to protect him. Skynet is much further along in time travel research, but not as far along in terminator design. Skynet has been sending machines back in time to conduct all kinds of prep activity to ensure Judgement Day happens and that Skynet will both be developed and will win the war. The Human resistance has been using time travel to insert operatives to fight Skynet in the past, prevent its development and generally muck up the works. Alison terminator sends Sarah, John and herself FORWARD in time 9 years to escape the Cromartie terminator.
Time Line 5+ - Here it gets really confusing because potentially EVERY traveler from the future is coming from a slightly different future based on changes being made in real time right now. For all we know, Skynet will be developed on the iPad this time around. Serves us right for letting Steve Jobs get so successful.