In some ways it would work, like the description I gave for the Red Eyes Black Dragon line above it. Blue Eyes too could have some kind of similar line I think. Same with Stardust Dragon, Red Archfiend Dragon, Cyber Dragon, and Galaxy Eyes Photon Dragon. Those kinds of monsters would have more multi evolutionary lines than any Pokemon before it. The Monarchs could serve a similar function to the Regis and I think there are mega Monarchs...which become their mega evolutions. I think alot of the bigger cards, like Chaos Emporer Dragon Envoy of the End and of course the god cards and their equivalents(like the wicked beasts and the avatars) would have to be the equivalent of a basic legendary Pokemon, also possibly Dark/Dragon. If there was a way to distinguish them I could see some kind of 'myth' built up around Harpie Girl and her ability to evolve into one of several Harpie Ladies a la Rotom (there are like six; original, sisters, 1, 2, 3, and Queen as far as I know) and it's further built up by the Harpie's Pet Dragon on some form. That's a new Pokemon movie right there.
Definently has interesting potential.