In terminator genisys we saw skynet assume the form of a t5000 impersonating a resistance fighter. Skynet injects John connor with nanobots turning John into a terminator.....
If skynet was that much more advanced than humans how did the human resistance even pose a threat in the first place?
Well that was in 1 single timeline. A more advanced timeline. In the original timeline, the T1000 was the a the most advanced Skynet creation and it was just a prototype. It was created right before Skynet was defeated. The T5000 does not exist in this or any other timeline before Genesis. Now as to why in the Genisis timeline, you gotta follow the number 1 rule in fiction: Don’t worry about it.
The franchise is kind of based on the idea that the universe always tries to get back to the state that it’s supposed to be, countering the „there is no fate“ idea that John and Sarah live by.
Meaning: no matter what John, Sarah or Skynet do, Skynet will always be created in some way but it also always will be defeated in some way.
It is one theory that almost always comes up in timetravel scenarios.
Maybe Skynet finds that merger repulsive, and only did it because John Connor had information critical to Skynet’s survival. Maybe under normal circumstances it would never consider that.