So simply put, the issue right now is whether they're seperate/unified enough to be able to put into (a) seperate/unfied thread(s)?
Laying it out
As a newcomer to this (as in, I was not present during last year's J/K saimoe), I would personally favor seperate threads,
because I do not know why the intertwining between two seperate discussions are necessary. And god, it's going to create chaotic discussions that cannot be distinguished between Jmoe or Kmoe, not to mention that I don't really care about Kmoe (or Jmoe).
Point: This is probably the biggest problem for a newcomer. Why the heck is it so important to link their discussions? Is it worth the Issue that it will spawn?
Issue: Confusion is guranteed.
Bob: "Huh? xxx isn't going against yyy!"
Joe: "He means Kmoe fool"
Bob: "Oh"
Tim: "Wait, yyy was in Jmoe?!"
Joe: "KMOE!
"
Spice to the Issue: This is not as important, but is possible. Someone who comes to the thread specifically for Jmoe wouldn't want to see Kmoe stuff, vice versa. That individual will become even more frustrated at the Issue.