I liked both seasons and they were good in different ways. But personally I thought the musical parody elements of season 2 were a bit weaker: having an arch satire of a musical that’s already an arch satire (like Chicago or Sweeney Todd) is a bit of “a hat on a hat” (compared to a satire of something more earnest). The parody of Pippin/Godspell/Jesus Christ Superstar was pretty good, though.
EDIT: I said as much in the dedicated thread for season 2.