Ideally a player should be able to fully configure everything in the pre-game time. Currently, there isn't enough time to do masteries properly and certainly not enough time to do anything related to runes. If you have to do any discussing or coordinating pre-game you will run out of time before you can redo your masteries.
Thus there need to be ways to configure things faster or there needs to be more pre-game time.
One idea to buy a little time in masteries is having shift+click fill a chosen mastery to the max or empty it out completely. If this is done on a mastery with a pre-req, it also automatically fills the pre-req for you.