Waiting for Godot consists of two men unable to act, move, or think in any significant way while they kill time waiting for a mysterious man, Godot. The characters fail to realize that this very act of waiting is a choice; instead, they view it as a mandatory part of their daily routine. Even when these men manage to make a conscious decision, they can’t translate that mental choice into a physical act. They often "decide" to leave the stage, only to find that they are unable to move. Such inaction leads to stagnancy and repetition in the seemingly endless cycle of their lives.
If Vladimir and Estragon realized they had the freedom of choice, they could break their daily cycle of habit and inaction. The problem is one of consciousness.
Vladimir and Estragon are fully aware of their situation and of their ability to choose, but the uncertainty surrounding the result of any potential action prevents them from breaking the stagnant cycle of their waiting.