To be able to make the skeletal animation from jMonkeyEngine work with the Minecraft engine would require some mad hacking skills and knowledge of the internals of the Minecraft engine, so I'd say no, its not possible in its current state.
The Minecraft code is obfuscated, meaning the author doesn't want people messing with it or modifying it directly.
To allow such extensive changes to the actual Minecraft engine would require either for Notch to release the source code or open up the Minecraft engine API alot more then it is now.
There are however modding capabilities that Minecraft does provide but if you want more (like the above) then you should request the authors to allow such things.
P.S.
You should also check out the javagaming.org forums for even more java game developers.