How different are the materials? Do they really need to be of different types... eg. Blinn changing to Anisotropic? This will be much easier to accomplish if you can stick to one material type. It would then simply be a matter of making all the incoming textures layered, and fading the alpha of the top layers from 0 to 1.
If you absolutely need it to be a different material type, the only solution I can think of is to have a duplicate object with the second shader, scaled a tiny bit smallerto prevent intersection. Then animate the transparency of the top object.
Good luck.
-Steve