Ensnare effectively balances retreat/flee. Trap aware is the only skill that voids it out and that is a skill specific to one or two classes. There are other ways to accomplish this concept. There are poisons that drain movement and stamina, leaving the player unable to flee. There are sleep spells that someone can cast on other, then load that player down with heavy items so they are slow. Those are the ones that I can think of right now. I don't see a reason to limit the number of times a person can flee in battle.
How would that be added in? If a player flees and meets the opponent again, an attack has to be initiated manually in order to start up a new battle so it seems to me that is a new battle. Would that start up the retreat/flee count over again? Or are you talking about limiting the amount of retreat/flee one player can do in a short amount of time?
Maybe adding a delay to the skill retreat since it doesnt take any xp away? That seems fair.