I loved Terminator Salvation, but I even I admit it had a lot of flaws, mostly because of constant rewrites and stuff. But the only thing that really bothered me was that Skynet seemed to know that Kyle Reese was John Connor’s father and was hunting him, yet when he captured him, he didn’t kill him. I mean, Connor said it himself “Kill Kyle Reese, reset the future. No John Connor.” Instead he used Kyle as bait. Skynet is a super advanced tactical computer, yet had such a convoluted plan. But I think I’ve come up with a theory as to why he didn’t kill Kyle Reese and his plan would make sense.
We all know Kyle Reese would go back in time, fall in love with Sarah Connor and father John. But, we also know that the Terminator in the original, figuratively speaking, fathered Skynet, because its remains were used to jumpstart the creation of Skynet. Killing Kyle Reese and preventing him from going back in time probably would’ve caused a paradox which would not only erase Connor’s existence, but Skynet’s as well. A risk that Skynet probably didn’t want to take. It would’ve been easier to kill Connor in the present than killing his future father and risk a paradox.
This might be a stretch, but it’s also possible that Skynet could’ve also planned to turn Kyle into a hybrid Terminator, send him back to 1984 to father John and leave Sarah to believe that her unborn son would lead the human race to victory, but only to ensure both Connor and Skynet’s existence and for Skynet to win the war.
That’s how I think it makes sense and less convoluted.