Flashes and stuns have many easy counters, the main one is positioning, if you position yourself in a place where you are safe if you get flashed, i.e. behind a wall or near one, and dodging flashes, by flicking away from them and anticipating scenarios where agents you are fighting are most likely to flash, e.g. through a door or through smoke. I play Breach and the biggest counter to all of his abilities is positioning, if you position yourself in a place where his abilities won't affect you then you will pick up an easy kill.