I'm afraid I don't know the answer. But thank you for asking the question. It is nice to see discussion about gameplay. I am looking forward to the responses.

Ninja,s Roundhousekick can counter every Jumpkick from everyone, you just have to do the timing right.
The timing is harder for Baraka and Shang Tsung but its very possible.
You just have to get the right timing.
You can also use Liu Kang Uppercut for 99% if the distance is not to great from the jumpkick.
And of course there are many individual Jumpkick counter like:
Baraka: Slice, Kitana: Zip Punch, or if you really quick Fan Lift, Millena Telekick, Raiden: Electrobolt and so on..
A straight jumpkick from everyone counters Baraka/Shang for the most times too.
Another good thing is to walk forward if someone constantly try to jumpkick you so that you walk under him and counter ect.
If you get some cheap (noob) players that try to jumkick you with Baraka or Shang to death, use a Ninja and Roundhouse them to hell, they will stop jumping after around 20 Roundhousekicks (my experience).

I play MKII like the AI plays it in Revision 1.1 and 2.1. Don't like the 1.4 one

I been watching Konqrr's mk2 combo video that stuff is amazing.I never knew you could do combos like that i tried some of them and there not as easy as they look actually there really hard.