Quake III Arena was pretty entertaining. Doesn't seem like it came from a company that had been ruined for years. I definitely noticed something around the Doom 3 release many years after Quake III Arena. The new game just didn't seem to have the same industry pushing, genre changing energy. Or maybe I was just older and had moved on, and didn't care as much.
It's not that the company was ruined, but that it had lost some of its creative direction after Romero left (while retaining technical excellence).