CHANGES
TheWB cut out a few scenes (including a big fight between Helena and Barbara), deleted vital segments of others. Many important bits of dialogs were left out. The way the re-shot Harley/Helena scenes were toned down basically undermined how the therapy allowed Harley to progressively get inside Helena's head and thereafter makes it less clear what Harleen Quinzel was. After the fact, it renders their ongoing sessions in the series next to meaningless.
In addition, the opening sequence with Alfred did not exist in the original version. The one thing that they shouldn't have removed about the original opener is 15 seconds of the young (10 years old) Dinah looking into the mirror with a blank stare as she said: "No, I didn't". I thought that was really powerful and revealing. That one scene was the most significant about Dinah Lance's character, it explained better than a thousand words how unhappy she was at the foster home and laid the groundwork for why she ran away in the first place. As it stands the revised version creates the illusion that her life at the foster home was *normal*, something which couldn't be any further away from the truth.
In the last Act, Ketterly got inside Helena's head using her greatest fear as a mean to destroy her. In the final version, we are not clearly explained what that fear is -- only that she doesn't want to be alone. In the unaired pilot, there is a shot of Barbara laying dead on a cold New Gotham street akin her long lost mother Selena Kyle (Catwoman). This image puts into focus that the real reason why Helena wanted to take her own life was that she didn't want to go through all of that again.