I've noticed that the Masterball is in my first slot when it comes to in-battle pokeball usage. Though using the masterball accidentally is minimized thanks to the usage prompt, it does get tedious to have to push down every single time in order to use a regular pokeball. While this is not a huge issue, having to push the "down" key, a say .2 seconds per key stroke, over 100,000 catches = 20,000 seconds. That means in 100,000 attempted throws, I've wasted more than 5 hours of game play.
Suggestion: Force the Masterball to be last slot in the users bag in battle