I will mention one thing thats bothering me. The increasing amount of Sub moves being used.
ie: use Flamethrower x3...except if your enemy uses something different, if it does then use..blah blah or whatever.
Ive seen some battles where a ref has to choose between 3 different attacks based on the situation. I can understand this being done by someone in the event of a Status change ie Use hypnosis 3 times till its effective, then use (whatever) since it doesnt always work the first time, or a pokemon that starts the round asleep could be ordered to use Snore x3 unless it wakes up in which case...etc.
But using it to try and gain an advantage and adapt to what your opponent is going to do shouldnt be allowed. Thats why we have the alternating attack system.