Not knowing much about the upcoming movie, nor anything about Bane the main adversary, I can only comment on the first two.
The choice of brown evokes grime and dirt and brooding menance - a perfect analogy of the scene in Gotham, particularly with The Narrows - a slum part of the city, a no-go area for police similar to the (no-longer existing) Kowloon in Hong Kong. The main adversary is Scarecrow, and the brown and black theme also evokes earthiness.
The brighter blue/red theme in The Dark Knight is perfect for the character of the Joker. The burning Batman symbol evokes a smiling Joker mouth, and ties into a key line of Alfreds:
Well, because he thought it was good sport. Because some men aren't looking for anything logical, like money. They can't be bought, bullied, reasoned, or negotiated with. Some men just want to watch the world burn