How come Skynet is still operational? Wasn't it destroyed in T2?
This is a major plotline of the series. Judgment Day still happens despite the destruction of Cyberdyne's program in T2. The origins of Skynet are shrouded in much more mystery in the series, as the Connors try to figure out what other technology programs might result in the creation of Skynet.This was a major theme in the movies as well: Judgement Day is stopped but another one is created a few years later by different events. The events which caused JD in T1 were not the same events as T2, or T3. Each film has had JD on a different day being caused by different set of events.Thats the entire basis for the storylines. JD is always stopped and a new one created.
What are the differences between the original 2007 Pilot and the broadcast episode?
Did any humans in the future help Skynet?
Yes. They were called "Grays" (i.e., John Smith is a gray). Grays are hated by other people, for obvious reasons, and usually are killed after being captured.