There are a number of different speaker cone materials: polypropylene, paper, glass, carbon and kevlar fiber, aluminum, and magnesium. And there is significant debate over whether the differences among them is audible. I have listened to enough poly, paper, and metal drivers to believe that I can hear differences among at least some of them. The reasons why they might sound different are widely discussed, but these discussions are usually broad generalizations. If any general rule does exist to explain why speakers with different cone materials sound different, there are sure to be many exceptions to it.
I know of one paper that begins to explore this question. It is a white paper written by Floyd Toole of Infinity. Yes, it has an obvious commercial interest to it, but Toole has an excellent reputation, and his work lays the foundation to why different cone materials may sound different.
Ceramic Metal Matrix Diaphragms
A Technical Report On Ceramic Metal Matrix Diaphragms
By Floyd E.Toole and Allan Devantier
http://www.infinitysystems.com/home/technology/whitepapers/cmmd.pdf