Comparing this to the Gotham Rail map
they produced for The Dark Knight, it would appear that they decided to put the airport closer to the coast, installing Gotham International in the location of the Brentwood Academy.
The geography is grossly consistant the Narrows has replaced Robinson Park. However, the layout of the city itself is drastically different, and the rail layout would seem to contradict what we see on screen in Begins
(the rail map shows a short direct link between th Narrows and Wayne Tower, while the first film shows a rather more complex route with at least two intervening stations).