I asked around for a way to combine 2d and 3d together and i was lead to this software known as TVpaint. I haven't have the chance to try it yet but from the looks of the movies done using it, it is pretty cool.

Here's one movie done by a Japanese man using TVpaint.

Link - http://www.youtube.com/watch?v=CXHUNtUIxeg

Previously i tried using photoshop for 2d animation but it is rather tedious.