A flash master piece if I ever saw one...
That was awesom. Great graphics, great fight, and great style. I enjoy watching stuff like that.
Now to get to what you could do:
1) Some people are complaining that nobody from MK wins. Here is my idea: have that idiot, Dan Hibiki, or some evil dude from SF fight somone you would consider good from MK (even though it seems obvious you don't quite like MK too much, but neither do I, so...)
2) Try keeping your story focused on being relevant to the first MK vs. SF you did, I mean, was this the real beginning or were you just making another story based on your first MK v SF.
Your submission was great, so if you choose to just keep having all sorts of SF guys beating the crud out of the MK guys, then fine, I'll probably love it anyway. Hope to see more from you...