Optimally, the best choice would be to learn all three variations for your character in order to minimize the problem of bad match-ups, which was the whole point in the concept. But for some of us, specific variations fit us better than others.
In my case, I prefer Ninjutsu Scorpion simply for the amount of range it allows me to control, as well as the conditioning that can be applied once the respect is there. I may learn Hellfire eventually, but Ninjutsu's options just strike a better chord with me so for the time being, I am a "variation specialist." LOL.
I do use Kitana with only one variation as well (Royal Storm). Like with Scorpion, Royal Storm adheres to a preference I don't think I'll find in Assassin or Mournful.