One thing I've always wanted to see was the Great Kraken as an Ammonite.
http://en.wikipedia.org/wiki/Ammonite
I find them much more interesting that simply bigger and bigger squids, maybe because I've actually held their fossils in my hands, but it would be fantastic if the Great Kraken could be a survivor of this extinct (as far as we know) species.
Another thing that could be fun is if there were some type of fossilized Ammonite underwater summons. Imagine a Great Kraken, only now it's made from living stone.
There are all kinds of really interesting extinct animals out there that could be put back into the game in various ways and forms, to very good use.