Crackpot theory: Ser Ilyn did not get his tongue removed for saying that Lord Tywin ran the Seven Kingdoms. Ser Ilyn discovered that Jaime and Cersei were actually Aerys bastard children. It would look much too suspicious if Aerys were to just kill him, so he said taking out his tongue was for saying that Lord Tywin ruled the Seven Kingdoms, despite the fact he had probably heard it a few times before from other men.
Ilyn seemed to get a kick out of Jaime telling him he was screwing his sister, and it was his own inside joke that he lost his tongue for. I think in the next novel Ilyn will find a way to tell Jaime of his true ancestry when he escapes Stoneheart. Ser Ilyn has served little purpose in the story, and I do think he'll serve a major role. I think I'm sold on Jaime and Cersei being Aerys' bastards. Jaime will find out about 1/3 of the way into WoW, and Cersei won't find out until seconds before her death when she is killed by Jaime, who already being a kinslayer, won't give a frick. In ADOS, Jaime will be revealed to be the third head of the dragon and one of the major saviors of Westeros, although he'll lose his life in the battle with them.
Plus the delicious irony on Tywin's grave that his only true born child was the mutilated dwarf he abused would be great.
This post was edited on 2/21 at 9:05 pm