Sorry, but some people need the time to think about prediction and mind games that often go on in pet battles. Just because it inconveniences you, doesn't mean the other person is somehow doing something wrong. Someone kills you at PvP. Sure, it inconveniences you, and now you have to spend more time to get back to your body etc. Should we take PvP out of the game? Of course not. And suppose Blizzard does see this as a problem (pet battle timer that is). What number would they pick from? Clearly they chose a timer that they felt wasn't long enough to be abused, yet long enough so as to give enough time to think and choose your next action. What is the time that would inconvenience you the least? 5 seconds between moves? 10? Will you come back and complain that someone is using all 10 seconds before choosing their action?
The timer is probably fine where it is. Just because you got 1 person out of a thousand to either purposely abuse it or simply use their time wisely to choose a move, that's life. We are all inconvenienced at some time or another. That doesn't make it abuse. Just move on. :)
If a person has let the timer run out multiple turns in a row they are either afk or attempting to grief their opponent into leaving.