I am aware that the current ("classic") rig has a lot to be desired. Instead of patching this old rig, I have been looking for alternatives. This can be seen in the different MHX files that are created upon export. Apart from the classic rig for Blender 2.4 and 2.5, there is also an attempt to use the Rigify autorigging system developed for the Durian project, see
http://durian.blender.org/news/rigify-auto-rigging-system/ . The rigify file is only half-finished (no skinning yet), and it does not seem to work as smoothly as I hoped, so we will see what happens with this.
Another really nice rig that I have looked into recently is the Gobo rig,
http://blenderartists.org/forum/showthread.php?t=172128 . This rig uses action constraints, so I must make actions and f-curves work in MHX before it can be applied to MH characters.
However, I don't plan to do much more work for Blender 2.49, because I have mentally already migrated to 2.5. There are also some rather annoying omissions and quirks in the 2.49 python API, e.g. no access to pole targets and copy rotation constraints always in world space, which make it difficult to make a good rig from python there.