That's most obvious in Movie 1 which went through several rewrites before the Mewtwo plot. Movie 4 went through similar things.
What sort of rewrites?
Also, @Atreyu: You mentioned that but no the Lugia vs Ho-oh scene? I mean, at least Ash vs Evil Ash could be chalked up to an early bit of the story involving Zoroark that got scrapped. The GS birds have no excuse.
Movie 4 originally didn't have Celebi in it. That was supposed to be for the anime.
Movie 1 was originally supposed to be an Epilogue for the entire Series.
Movie 4 originally didn't have Celebi in it. That was supposed to be for the anime.
You also seem to confuse "the writers brainstorm somewhat to come up with a plot for the next movie" as "the movies go through several heavy rewrites".