My Ideal structure for the NY City Council
Basically keep the 51 Council districts, but add 13 apportioned borough seats (minimum of 1 per borough) using STV for those that fail to make the minimum vote cutoffs, and then do the same thing for the at large seats. Or you can use published party lists.
O, and a minorities law(similar to Puerto Rico's) so if one party gets 2/3 of the seats without 2/3 of the vote the party that came in second gets the same number of seats as the amount the winning party went over the 1/3rds limit.