I agree the writing this season wasn't as sharp or focused as the first, but you misunderstood the ending. William was not a host, and I'm pretty sure his daughter wasn't either. The dude was paranoid out of his mind to the point where he shot his own flesh and blood daughter just because he THOUGHT she was a host and part of Ford's "game." The whole scheme with Dolores-as-Hale at the end was one of the better written twists this season if you ask me.
Bernard responding to "cease all motor functions" stumped me, too, and Ronin world did seem kinda pointless in the end, though I suppose we did get some character development from the whole ordeal.