A couple reasons:
First is I didn't decide to have a cartoon in it until the script was done, it just kept evolving and I had skills in animating, so I treated it as sort of a prequel to the film. This was all done on my own budget so I had limited resources.
Also, I thought going back and forth between animation and live action with no purpose might be confusing.
But my next project I am playing with the idea of a character who gets sucked into a cartoon universe, so it may work a lot better that way...