Enter Vulture's interview with former Dawson's Creek showrunner Greg Berlanti, who talked about the change-up that occurred in Season 3 to make the romance a reality.
When Berlanti took over the show from the series' departing creator, Kevin Williamson, he knew his goal: "I would get Pacey with Joey and have a King Arthur–esque story."
"Dawson being King Arthur — exploring what happens when Lancelot and Guinevere fall in love," he told Vulture. “[Joey and Pacey] always had such wonderful chemistry, the two of them — they have a Tracy and Hepburn quality that I liked writing for.”
And so it happened. As Berlanti notes, “We just wanted to write what we wanted to see."
When Williamson made his return for the series finale, he gave his approval of the storyline by writing an ending in which Joey and Pacey end up together. As Williamson once told Entertainment Weekly, the beauty of the dynamic was always there.