Wall Worm 2.331 was released yesterday. The update has important changes to the way the SMD exporter works. It will now export bone systems in a more expected manner with less need for the user to understand the way the nodes/transforms have to be setup for WW. In the past, many hierarchies could get bad transformations if the nodes added to a WWMT Helper (or SMD Exporter) were not set up a specific way or added in a certain order.
In all the tests I came across with many user-supplied files, this update solves all the problems I could solve automatically.
So hopefully this will make exported animated models less of a hassle.
I also need to clarify something that has been noted in the past but not made explicit enough: the WW SMD Exporter fully supports only 3ds Max 2014+. This is because when Max 2014 came out the methods for interacting with Skin modifier data was drastically altered. When I added support for 2014 I inadvertently broke the older versions of Max. By the time I figured this out, there had already been many layers of changes... and I have never had an incentive to go back and fix those. So if you find that models with Skin modifier export with incorrect bone weighting, it is probably because you are using an older version of Max. I recommend getting Max 2014/2015 (as they are much more stable and fast than 2012 which is what so many Source modders seem to be stuck on.)
I have updated the docs on Exporting CAT and Biped Models to reflect the current version of WW.
Please report any bugs you happen to find.