Most of the important mysteries were addressed actually. A few of them weren't addressed onscreen but nearly all of them have been answered somewhere.

The ending makes it pretty clear that most of the plot had been planned out pretty extensively from nearly the beginning of the show. There is an astounding amount of foreshadowing that viewers will not notice the first time through because of how complicated and unpredictable the story was, but a second viewing will reveal just how much of the plot had to have been planned from the start.