The reason the pilot was so long was because, unlike every other episode of the series (which is created using software made to look out cutout animation), the first episode was actually made using cutout animation, which took quite a long time to make.
Sure enough, it took quite a long time to put the first season together.
Specifically, it took three months to make the pilot, “Cartman Gets An Anal Probe,” with a small team of animators.
Thus began Matt Stone and Trey Parker’s working relationship with Comedy Central, and the early days of South Park’s soon-to-be long stay with the station.