technically this isnt MK3, it's a restart...I personally think that the basic storyline from the original would be ok to use, but it needs to be longer, and you need to have some sort of b-plot going on as well.
so what you do, is you have quick backstories at the beginning for the human characters. You see Liu Kang training to go over, the one true believe in it all that he was in the games, you see Johnny Cage signing up for being bashed in the press, you see Sonya's partner getting killed by Kano and her going after him...but you start it all off with what everyone wants to see, Scorpion and his family being killed by Sub Zero and the Lin Kuei, and him coming back for revenge...then the only characters you have to set up are Raiden, who would be pretty much like he was in the original movie, a guide, and Shang Tsung and Goro, who dont really need that much character development...once you have the motivations down, the movie would pretty much write itself.