I might as well give my two cents on the subject.

I have no preference.  Each way has it's benefit.  Script format tends to
create an ambience quite similar to the television show.  There is an
emphasis on the conversation and dialogue to carry the plot. In addition,
readers are offered an exact description of the physical events of the
environment.

Prose is a much different matter.  It doesn't give the feel of a television
show, and it offers a way for readers to get into the heads of characters.  

Otherwise, I don't care what format fanfics come to me.  I read everything.
Of couse, I prefer to write in prose.  It looks more impressive :)

Michael Chen