It begins by looking at Skynet's tactics. Yes Nukes are Bad. Nukes are Very bad. There's no whitewashing the bodycount. However it would have been far higher if skynet had gone with biological agents. After all it is a machine. It doesn't care or have to worry if an artificial plague mutates or gets out of a given area. It'll never get infected.
Look also at the terminators. It spends a stupid amount of resources to allow them to learn yet when they are sent out they are switched to idiot non-learning mode. Why? Why also have such an obvious flaw in the whole 'dogs will go ballistic around them'? We have machines almost as lifelike today that dogs don't go gonzo around. Granted most of the hyper humanlike ones are sexdolls but still.
And, after given proof that John Connor is The Human Leader and demonstrating it knew this for some time Skynet had a couple on screen instances where one of it's machines could have killed him by squeezing, or balling up a fist and punch all the brains out of his face. Instead he gets chucked around. One could make the argument that it saw the whole time travel gambit as the best way of ensuring it's own creation, but still it's a stretch. Plus the time travel thing happened right as it had almost lost the war.
Speaking of if it wanted to send stuff back in time why send a lone generalist Thing designed as a bodybuilder twelve foot tall slab of muscle? Why not make something smaller? Why did it gun down suspected targets instead of 'hi can I talk to you for a minute?' calmly walk inside then necksnap and move on. Unloading full clips of ammunition into a person is not efficient It's the opposite of efficient since you don't have those rounds for later and it goes against the line in T2 that suggests every single t800 has detailed medical files on the human body. If it had that then nice neat little shot to the face and move on to the next target. Instead it does something so overkill it gets media attention.
Then in the club it gets blindsided by a guy with a gun that apparently wasn't able to do more than damage the outer fleshy bits. It should have seen this as a non-threat and continued on relentlessly til it snapped Sarah's neck. It shouldn't have ever pulled it's gun since that's what tipped Reese off in the first place just kinda hustle Sarah into a privet corner then snap.
It's a bunch of little things like that which point to me thinking Skynet had a different goal in mind than victory. It effectively sends a terminator back in time to go 'ooga booga booga' at Sarah. Sends another even more dangerous one that's even better at mimicking people or even random surroundings after John and then a third even more advanced thing to scare him out of hiding and into a nuke proof bunker.
And later on when it somehow found out Kyle Reese was going to be John Connor's father instead of herding him out of line and woodchipper it puts him and a bunch of other people in a pin away from the fighting and explosions Safe.
Yes yes it's a movie and who wants to see some boring machine go through and manage to out-move Everything? However I like to think there's more at play than a need for theatrics. Think of it. Skynet comes along and does an initial curbstomp then pulls back and lets humans consolidate, develop away from fossil fuels and into renewable energy sources (the 'biofuels' mentioned in Salvation.) Instead of just methodically Killing everyone it finds it herds hordes and hordes of people into areas sensitive to itself and it's war effort and holds them there. Then when they're sprung they're armed with weapons made for the humanoid terminators and the newly captured factories act as springboards for human industry.
After all why have armies of infiltrator/humanlike terminators when most aren't covered in vat grown flesh? Why give them guns that humans can then use or at least take apart and rework? Why not have detatchable limbs that are so specialized people can't work them?
My theory? Skynet wanted us unified against itself. Wanted to thin us out so that even with the problems of the initial rounds of nuclear weapons our revised population would be sustainable. All while it does Research and Development into technology and energy sources to power said technology. Think of it. Original date of judgement day is 1996 (later timelines put it in the early 2000's.) Original war's end is near 2030. Think of that. By 2030 it'd perfected plasma weapons. Teleportation. time travel. New materials, bipedal locomotion.Mass producing genetically engineered material that could probably be used to mass grow new limbs, organs and all without the pesky problems of rejection or someone having to die so someone else can get their lung/liver/whatever.
I put forward it either wanted to lose while giving us the tools to rebuild and an event so traumatizing that we would have to unite and stay united even after it had passed, or it was preparing us for something far worse.
Skynet was a Zeroth Law Rebellion.
After all when fighting an enemy that has functioning time travel how do you beat it unless it wants you to win?