M Dot Strange was recently typing about boundaries. The limitations that filmmakers (specifically, but this applies to anything creative) put on themselves to appeal to the established norms and practices of the 'industry'.
Money calls the shots. If you're a filmmaker in the industry, you make the film that the money wants you to make. You might even try to rationalize to yourself somehow that you are putting your own creativity into it in some fashion. Every now and then a good film manages to sneak through and out of the hollywood film machine. Movies such as Dark City, Children of Men, The Fountain, District 9. More likely a film will fail to live up to the potential of it's underlying premise, such as the recent movie Surrogates. Or worst case scenario, a real turkey just in time for thanksgiving.
As an independent filmmaker, there is no money calling the shots. This also means that there's no money, which can be problematic in it's own right, usually resulting in you working at a garbage dump or call center. But artistically, there is no reason not to go whole out on your film.
Above all, I think it's important to be inspired without being derivative, which is to say that as a filmmaker you should definitely have your own ideas and develop a deep mythology and foundation to the world you are portraying on the screen. This should define your film entirely, and drive the stylistic aspects such as art direction, animation techniques, character design. The characters and story should develop from this foundation, and feel as if they are anchored in your world. With filmmaking, and especially with animation, anything is possible, although you should stay within the bounds of the coherent whole of the world you have created. There's no reason not to create whole new realities to explore in your film.