Interesting that you're not enjoying Thomas's part in the story. I really like the parallels between Bruce and Thomas, and the relationship we started to see in Beasts of Burden.
Bat/Cat isn't resolved, though - that's kinda the point of doing a 12 issue series to wrap that up.
I think Catwoman has never had the same connection to Gotham City as Bruce, but I think she's often made it her mission to make it better - Valentine's run was all about that, and Brubaker's run started with that idea for her little space in Gotham.
Interesting. I know Thomas was re-introduced in The Button, but I've never thought he was going to be a bit part of Doomsday Clock, since he's such a huge thematic element of King's run.