I think that while i like The Pilot, it, alongside The Thing You Love Most, are the two episodes that cause the most long term plot inconsistencies for the show. At least back then. Now everything the characters do is pretty much inconsistent with previous characterization and the short term plots have no connection to the near past of the show let alone the far past of the characters lives.
But even back then, you can tell that the writers were not keeping track of their timeline and would throw out dialogue that was inconsistent with future events that happened in the show.
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