There are plenty of FPS games with AI that you can control with commands. The Rainbow Six games all have this, and if I'm not mistaken, I believe Counter Strike's bots can be controlled with commands as well.
Quake III's AI not only receives but also gives commands by chat. If you enter a team full of bots, you can see them talk to each other and "plan" to a certain extent.
Hah! Quake 3 and UT99 both were helped immensely by having the ability to command bots--that often would be the difference between a stalemate in a CTF map and a flawless victory.
