Yeah, the leading figures in the first game story-wise were Tetsuya Takahashi and his wife, Soraya Saga (lolz Saga working on Saga), who worked on the story together. Both were asked to step down from their prominent roles in the series after the first game failed to sell as much as expected. Yasunori Mitsuda was also kicked out as composer, and Yuki Kajiura was brought in. That one admittedly wasn't so bad.
The rest was apparently a mixture of their original story and the vision of the new director.

To be honest, though, the story felt pretty consistent to me throughout, and I don't think it suffered so much from the new director as from poor sales causing it to be cut from six games to three, and thus the necessity to summarise like...everything.
...
So let's blame people for not buying the first game?
