Thematically, it just makes sense.
When the series begins, Gotham City is incredibly corrupt and crime is rampant. Wayne Enterprises is run by a greedy CEO. Gotham City lives in fear, and the League of Shadows has deemed it so far gone, that it must be completely destroyed.
Then Batman arrives and starts protecting the city at the street level. Harvey Dent arrives and starts his war on crime on the more official level. Now instead of every citycitizen being a victim, you have many standing up to do the right thing. Bruce Wayne has turned Wayne Enterprises around. Gotham has started rebuilding itself from the ground up.
By the time Bane shows up, Gotham has made a lot of headway. It's the sort of big, successful city or metropolis (not to be confused with the city) that one typically identifies with modern cities such as New York.
You also have the whole dark-to-light theme of the series. Gotham starts a dark, dangerous place and becomes a bright and shiny place full of hope. This is expressed through the story itself, the color/lighting scheme and even the very design of Gotham City.