Some of the choices were for the better. The chapter with the Avalanche crew, for example. Or the extra time spent with party characters, which contributed to really good character development overall.
Other ideas were interesting in a vaccuum but not really well integrated into the story, like the ghosts subplot in Train Graveyard, which was anti-climatic given the context. That is more a consequence of the original game's plot in Midgar being really tight, so adding new stuff into it was bound to not always succeed. I don't expect this to be a problem in future parts, though, because the original story has a much looser narrative after Midgar.
I think the additions that really hurted the story the most were the whispers (that was totally Nomura's idea, btw. He himself said so in interviews). The whispers exist specifically for the last chapter, and were kind of tacked on for most of the game to remind us that "hey, they exist and will be important sometime later!" Their importance in the story and for the future of this project is clever, but the execution felt rushed, as if the writers had decided to add them late into development.
