I saw the Dollhouse pilot on the season one DVD. Having being a fan, seeing all the episodes, also season two, I understand why Joss Whedon decided to re-do the pilot and shoot a new 1st episode. The pilot is confusing, only understandable about fans. It is like chess pieces, some pieces are ahead of others. Joss probably wanted to go in another direction, he pulled things back and pushed things forward. The pilot shows off as a showcase to Eliza, but not much of a conscious one to a new viewer. Also, certain rules have changed and they were feeling things out as they went along.
For example, in the pilot, Paul Ballard is only getting started. We are revealed in the pilot that Victor was programmed to trick Ballard, but it took about five or so episodes to reveal it in season 1. Echo is actively programmed to kill Paul in the pilot, but not so in the first episode. Things with dr. Saunders are pushed forward in the pilot and pulled back in the series, spread out. Also, Sierra is already an Active in the pilot but is a 'new' Active in the first episode. The first final episode is more polished and better to understand.
For example, in the pilot, Paul Ballard is only getting started. We are revealed in the pilot that Victor was programmed to trick Ballard, but it took about five or so episodes to reveal it in season 1. Echo is actively programmed to kill Paul in the pilot, but not so in the first episode. Things with dr. Saunders are pushed forward in the pilot and pulled back in the series, spread out. Also, Sierra is already an Active in the pilot but is a 'new' Active in the first episode. The first final episode is more polished and better to understand.
