Only a couple of scenes (or clips, rather) are pre-rendered, and iirc they don't have any characters in them. All character cutscenes are in-engine.
Xenoblade X also has some absolutely amazing cutscene animation, but it is sparse, and some can be missed due to being in optional quests and the like. Their next game should see even better animation all round; they used a special suit for a lot of the in-game animation (battle animation, basic animations, etc, the big cutscenes were mocap) and they got their hands on newer versions of the suit before finishing X, which they'll be able to use throughout their next project.