As far as I know one of the MK co-creators was working on the script for the movie. I guess they thought that whatever crap they will produce, power of the brand will make it profitable. Besides, nobody expected that first movie will be succesful.
Another big problem with the movie was that it was directed by the operator of the first movie. Paul Anderson quit from being director, after writers refused to change script whatsoever. Change of actors and lousy special effects didn't helped either.
I've read several fanfics that were written better than MKAn...
