It's because the pairing naturally had two outcomes that was tied to the fate of the show.
Pokeshipping was basically canon and anyone who disagrees with that assessment must have been completely blind because practically everyone who watched the show knew something was between Ash and Misty, and it was only a matter of time before they confessed/kissed/etc. Kanto/Orange Islands pretty much gave all the hints needed. And by the end of Johto, their relationship had gone on for so long that it was the only thing left to happen.
Problem was that is end-game stuff, and left only two options: complete Ash's story and have him and Misty live happily ever after, or write off Misty and continue Ash's story endlessly. They chose the latter, and ignominiously ended it with "Now I know how you really feel about me, Ash" that basically spelled out their mutual feelings for each other but left it without any resolution.