According to Jeremy Linden, there are plans to have animated mesh without relying on the avatar armature.
http://wiki.secondlife.com/wiki/Why_UUID_Flipping_is_Bad
However, that was back in August of 2011, and I'm trying to see if anyone has any information on when/if this is actually coming. I have not been able to find any recent updates on the subject, even though it's something that could be essential for the emerging products and markets in SL.