I dunno, S1 had some great twists with the nature of Bernard and who the Man In Black was, when you can tell a story that spans decades and not tip off the viewer thats whats going on because most of the people involved are ageless immortals in an environment that never changes, so I wasn't expecting anything that well executed in S2, because its a great trick, but you can only pull it off once.
My only real complaints with S2 were that the shogun world tour was basically pointless filler, and that they walked Maeves character back from where it logically should have gone, presumably because they didn't want to make her the actual star of the show.
Thematically, choosing a freedom thats really just another prison, just one where you can't see the bars makes sense. So does touching on free will being mostly an illusion, and that the humans are just as programmed in their interactions and responses as any of the hosts are (and heavily implied, human programming free will is even more simplistic than AI).