Del Toro plans to use Peter Jackson's films "as canon," but there will be changes afoot. As Eugene noted earlier, there will be a different color palette for the world of the hobbits, and instead of inundating us with a film full of stunning CGI, Guillermo is anxious to make a lot more use of animatronics.
Will this change only be subtle, or will it look like an entirely new film that only has a few familiar faces? It's certainly possible to make a film that visually fits -- each Harry Potter director has added touches to their films to make them stand out while still creating a cohesive series. However, we've got to keep in mind that the seas haven't been smooth where Peter Jackson and this fantasy world is concerned. Eric Kohn brought up the "smells of George Lucas" thoughts in his post, and you have to wonder if Guillermo will be free to build his world in peace, and if behind-the-scenes issues could tarnish this whole affair.