Having served aboard several "ships" like the Midway, Constellation and the Coral Sea I can understand why the Enterprise in this movie version is so different.
When the Midway was first commissioned in 1946 it had pretty much of a straight looking flight deck and also it had been initially constructed to be a battleship.
Throughout constant retrofitting and upgrades the final product barely resembled the original by the time it had been decommissioned the 2nd time and now is tied up to a pier in San Deigo, CA as a museum much like the Intrepid in New York.
The TV series started out pretty much with Kirk in his mid - 30's, so it is conceivable that the Enterprise had gone through many upgrades etc. After all look at what Willian Shatner looks like now!