<Snipped quote by Rin>
We can still just go with the alternate universe. The fact is, MKX is relatively new and if a lot of people haven't played it yet then it will be hard to base our story off of it.
The idea of starting the story after the first MK makes sense, leading into the events of MKII. It would be much more accessible to people.
And their choices would carry over into something different.