Taking into account the idea raised about speed (that is, that a slower substitute is far more likely to get the job done), I suppose a better Nature for Kojondo in this set would be Relaxed, Sassy, or Brave (cuts Speed, raises one of his more necessary stats)
Or would a Speed raising nature be better of Kojondo's mind games? Either way, Relaxed/Sassy/Brave would be alright for Kojofu.
I'd definitely use a +ve with Kojondo, if you want a slow Sub passer go with his Prevo. It lets him revenge a lot of things nicely, and although a fast sub isn't ideal the fast U-Turn is essential to force your opponent to predict.
Not to mention, it doesn't matter too much if your Sub is destroyed by a prediction, the next turn you can simply U-Turn away anyway to recover the lost health.