Skynet only had 1 T-1000, it was the most advanced thing it had and it sent it back because it thought that was the best use of the tool. Its other assets were things like giant tank robots and nuclear weapons, it had more and better tools to work on a large scale than a small scale. Its boots on the ground were robots with laser guns, which humans could hide from. As described in the first movie, infiltration of human communities was a weak point for it. T-1000 was impressive, but if Skynet only had the resources for 1, how much of a boon is that really? How long did it take to design morphing metal? How much metal suitable for that task could it even make?
Just because Skynet has theoretical technologies it could design doesn't mean that it could build or use them. It still exists on Earth (and maybe further out in the solar system, that's never been discussed to my knowledge,) it still has to deal with gathering materials, testing new ideas, figuring out which technologies it can use practically, and getting the resources it needs in place where it can use them. It still had to deal with logistics.