There were definitely mysteries, and most of them worked.
William becoming the Man In Black is one that didn't work for me. I liked both characters but his transition from mild mannered wannabe to one-man killing machine overnight (literally) was too much for me to believe, along with the idea that he'd push Logan aside once they got back to the outside world. Logan is a jerk, but back on his home turf I still think he'd have eaten William for breakfast.
However, the show, overwhelmingly, achieved it's goals. I think it should do well at the Emmys for example, especially for the cast, but really anyone who worked on that show should be proud of it.
I am really impatient for season 2.