Originality is almost impossible to achieve ever, its the way you do it that matters. The Matrix was not original, there had been many ideas brought upon that before it as well.
Thinking how computers run....on a program. Just like humans have the program into them to mate and carry on genes. It happens, it's ******ed, and really has no purpose other then to spread. That is no different int he programming of Skynet, its simple, and may sound stupid, but that is possible how a machine like Skynet may think. He follows his programing so much he does some odd things, and interprets programing different. As humans do with many things themselves. Cameron just tried to think, if a machine was made to protect the US and saw how dangerous we are, would he interpret it differently? As many humans interpert other things different, like religion and so forth. You say it seems to easy. Sometimes the easiest answer is the most likely. Just because it is easy does not make it any less complex of a reason, or most of all , "powerful" of a reason.
What the point of that was above to say it may be easy. But sometimes the most powerful things in this world are simple. And that was the creepiness of Skynet. Just a simple thought that terminated most of humanity.
Now of course I'm not saying you are unable to believe what you believe. But every thing you have brought up I have given a rebutal that is within the films themselves. And explanations. If you still don't like how it went that is fine, to eaches own. But there is reasons why these movies are still seen by many sci-fi lovers as masterpieces.
And as for there being some "but" moments in the movie....99.99999999% of fictional stories have that. No matter what. Some just make them more believable then others.
If you wish to continue this discussion and have a PS3 I would gladly do so verbally.You seem like a very intelligent chap and these discussions have been fun. If not well this has been a fun board discussion/debate.