I think people have simply been breeding dogs for very much longer than cats, so much more extreme variations have been produced. Certainly there are cat breeds that are now linked inherently with potentially severe health problems, like the Manx: http://fanciers.com/breed-faqs/manx-faq.html#medical
I certainly haven't seen any evidence of "extreme" MCs being subject to any special health issues, so I really have nothing against people breeding them. I just believe that cats that bear little resemblance to the MCs that arose naturally should not be sold as being "Maine Coons."