I just finished reading what’s described by Daily Script as the final network draft of Supernatural’s pilot episode (http://www.dailyscript.com/scripts/Supernatural-1.pdf
Chunks of it made it to the screen: Mary's discovery of the man in the nursery, dialogue between Sam and Dean when they reunite, when they hit the road and when they wrap the case.
But there are major differences, too. The ones that stood out for me:
1) In the opening flashback, blood drips on a Sesame Street blanket, not on baby Sam directly. The aired version amplifies the irony and the horror of a murdered mother's blood dripping on her smiling, happy baby. Having the blood touch Sammy directly opens up the reading that Sam was infected by that blood. It is also an extention of the blood = infection = AIDS metaphor that dominated horror in the 1980s and 1990s.
2) Sam takes more of the positive action (finding things on the Internet, persuading people to cooperate, deducing things about the case, scamming his way to see a prisoner in a scene that did not make it to the aired pilot). So all the "action" is of the intellectual kind. Yet, he doesn't actually solve the case. Constance's entire backstory is told to him.
3) While Sam's intellectual skills are shown, Dean's physical prowess is only hinted at. This is the reverse of what most shows do: it's easier to show badass punching than badass research. At one point, he only acts when Sam tells him what to do, but Sam only knows what Dean should do because someone told Sam. Passivity begat passivity! Also less dynamic was the scene where Dean reunites with Sam. There is no fight. The fight showed both boys' prowess and introduced Dean as a man of action.
4) Sam and Jessica are just dating, not living together. Their negotiation about how to take the next step (meeting her parents) overburdened the script. The decision to show Sam and Jessica together in the apartment they shared created a parallel to John and Mary's home. Sam is shown to be making a family of his own. So the episode began with the loving, protective Winchester family, then the loving soon-to-be Winchester-Moore family, then questioned John's decisions as a father, then introduced Constance as an example of a protective parent who went overboard. As a result of her somewhat justified obsession, she physicall killed her children. As a result of his somewhat justified obsession, John was stifling his children.
5) Constance's interactions with the first victim in the episode and with Sam in the car later on are very close to what aired. However, her entire backstory is different. It is not tied to any specific myth or urban legend, although at one point Sam says there are a lot of legends about ghost hitchhikers. Because her actions aren't tied to any particular myth, she is like a character from Criminal Minds, a psychopath whose story doesn't have a lot to say about anything else. (Her story could have been tied to LIzzie Borden, though.) Giving Constance a backstory rooted in myth reinforces the show's premise. It also reinforces the underlying theme of what parents will do, however twisted, to protect their children.
Obviously, I'm biased because I've seen the pilot many times, and I've seen the stories that were developed from details in it. But I do think all the changes made the script better. They made the characters more active. They introduced additional layers of story. They drew direct connections between the Winchester family melodrama and mythic stories. This allowed Supernatural to use the procedural format, but to transcend procedural stories. It was the beginning of the epic story of Sam and Dean Winchester.