I arrive after the battle...but for me the Mugen 1.0 is better than
Winmugen because as ArkadyRossovitch say it so well, Mugen was built
and optimized under DOS and Winmugen is always a beta.
Mugen 1.0 require less memory so the characters work better.
But it is true that a lot of characters don't work under Mugen 1.0
as emphasize it Snakebyte.
Moreover now the most of the creators use Mugen 1.0 as base for
the creation of their characters. Because under Mugen 1.0 the
characters "weigh" much less than under Winmugen (15, 30 even 75Mo).
Now everyone will choose the one with wich he is most comfortable.
It is necessary to know that it exists dos2win, a little soft
to convert DOS mugen (Mugen 1.0) character to Winmugen character
and a french/english docucument explaining how to convert a winmugen
character to a DOS mugen character. Document created by Mikemugen.