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The only disadvantage bots have that I can think of is that they can't (I don't think) discern when their opponent is on tilt.

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Bots will be able to tell when people are tilting, why would this be different than anything else? They just have a player model that incorporates both short and long term patterns in another player's game.

Bots will certainly take over; it is only a matter of time. Like someone else said, if sites implement bot-finding technology, people can just run the bot on another computer and input the actions. There is absolutely no way to stop this.