Go for season 3 hands down! It pushes the substance of the series into every dark smelly crevice you can think of. Also Black Museum; it's like three episodes in one, and touches on a lot of the ideas that other episodes are dedicated to.
I totally agree - there's a hopeful vibe to the latest season, which is a bit of a departure from what we usually get. I found the first ep strangely endearing, the other two sort of stale.