The choices matter but more so to customize the experience to the reader moreso than completely changing the story. The plan was to have two "perspectives" rather than actual separate "routes." This basically means that the story is written one way but based on your choices and perception, it can chance things. We haven't gotten to the biggest difference between them but there are very subtle differences already places throughout the game.
In terms of the ending, there's no way i could spoil that. I've always answered that question as this: "I feel the ending will be appropriate for the journey we've been on." It must fit with the story or nothing mattered the entire time.