The ending was not the best, nor were many parts of the middle. The story really seemed to pull stuff out of it's rear far too much. My son's interpretation was that Inori is now inside Shu, having combined with him to save his life, or something like that. It kind of gave the impression that he is able to "see" her in his mind.
It wasn't the best series, but it had its strong points. Killing the prettiest girl of the anime season wasn't one of them!