Well, its the nature of the counter game. Due to the fact that your playing a game that forces your opponent to essentially be hit by any of your moves, having something like Toxic, Will-o-Wisp or Hypnosis on your pokemon basically shuts down alot of counters, and forces you to either choose a new pokemon or use a lum berry. You'll also notice an increase in the use of Substitute due to the fact that you can guarantee yourself the ability to use it.
It seems the basic idea when making a counter at this point is to chose something that can easily counter the current pokemon with one move, then give them moves that they wouldn't normally be able to use, like rock polish or swords dance, then another move for type coverage then a final move that will either guarantee perfect type neutrality or, if you cant manage that, either Substitute, Hypnosis, or one of the other useful status moves they learn.