Thats up to you. Personally, I still use it. Here's why:

-The new MS3D does import .skn files now, true. But did you notice that they are positioned a bit different in .skn format than they were with .obj format? The arms reach up and are twisted a bit. The head is tipped back, too. Makes arm meshing a bit more difficult, if you want to scale out arms or sleeves. It doesn't work the same any more.

What I do now, if I need to do that, is do the rough meshing, adding, etc. for everything else but the arms. Then, I export the .skn file, load up SKN2OBJ and convert them into the project files. From here, you can easily edit the arms as you like, export the .obj back and convert back to the .skn format. Arms are now fixed.

-With the tipped head, hair meshing is more difficult. So what I do is mesh the head with a base .obj file, mesh it as I like, then import the same base head in .skn format and move my new head into position, tipping it back untill the base heads match up. Then I delete the base head .skn file assign the head to the head joint (more on that in an upcoming tutorial on Joint Assignments) and export the new head. If the hair is longer, you can move the base of the long hair into place here as well.

So keep it or lose it, it's up to you. But sometimes it's just more useful to have it just in case. :)