i agree with Kebren. I now open up a window on my poketeam, then throw a pokeball. If the window closes, i know I caught the pokemon. The battle doesn't sync with any of the information outside the battle window: xp goes up right when I click the action instead of when it actually happens; pokemon appears fainted in roster before your pokemon actually faints; if you have an empty slot, caught pokemon appears there before the ball animation ends; on a full roster, if you have a status window open, it will close when a pokemon is caught, even before the animation stops.
These little things aren't bad, but will greatly improve the finished product and make it more polished.