Let's take a moment today to think about the shifting status of the pilot episode on American television -- a worthy topic in the midst of the rolling out of a battery of new television shows across the various networks.
In the past, the pilot served very specific functions within the behind-the-scenes decision-making at the networks. We might think of the pilot as functioning in television the way that a character sheet functions in comics or animation: it seeks to define the core characters and central premise of the series but it also does so by pushing them into their most extreme versions. The characters in pilots are often over-defined to the point of being reduced to stereotypes as the producers try to show who these people are, how they relate to each other, and what functions they serve in terms of the plot.
Compounding this problem is the degree to which performers have not yet fully jelled with their characters -- in many cases, they may have just received news that they were assigned these roles and been rushed into production on short notice. They are trying desperately to prove they can act so they can hold onto these parts. In the past, it was not at all unusual to recast key roles after the pilot was shot and before the series reached the air. In any case, we know that character on television is generated as much by choices made by the performer on set as they take up the roles as written and make them their own and typically it takes a few episode for the rough edges to give way to more fully human characters. (Of course, the opposite can also happen and a compelling character in the pilot can be smoothed out or compromised through the production process.)
Radical shifts in the conception of the series may occur after the pilot has been shot (see, for example, the case of classic Star Trek where Spock was a highly emotional character in the pilot and Number One, a character cut after the pilot, represented the voice of cold rationality). The pilot was almost never a particularly strong episode from the point of view of the audience but producers and network executives knew how to read pilots, or thought they did, and used them as tools to make decisions about the show's fate. It would not be rare for the pilot to get shuffled into rotation later in the run of the series (again, Star Trek is the classic example here where the original pilot got reframed and turned into a two part episode -- a flashback -- later in the run of the series). There was a clear separation between the pilot and the first episode.
And all of this took place behind closed doors. Network executives saw lots of pilots; they knew more or less which ones turned into good shows down the line and they knew what were the symptomatic rough spots experienced by most pilots. They might be anxious about innovation and shut down shows which took them in new directions; many of those shows are more likely to be embraced by at least cult audiences than network executives, but for most series, they knew what they were looking at when they saw a pilot.