In the movies, Celebi was a pathetic damsel-in-distress type who had to be continually scolded and tamed for the benefit of the 'protagonists.' It's no surprise that they soon happened upon romance plots where the Pokemon might ambiguously play the female part. They could hardly do significantly worse.
The movies aren't in principle outside of the anime's canon, as for instance in the first movie being foreshadowed by Gary's problems in the Viridian Gym. The G/S ball was quite badly handled, in a way, but they might not have really figured they would be able to make a significant reveal there, especially with the protagonists of the series being portrayed as fairly ordinary by that point. Interest was also declining slightly in the elements of the anime added in the Johto series, and as such they might not have wanted to too blatantly recognise having a more niche audience than the previous region, which is generally more associated with the anime. You could say that it was abandoned somewhat, like the Ho-Oh thing was.
