Theres definitely uses for EX Thunder Knuckle. If someone misses a Rush Super like Balrog or Chun, you can jump over it and then while they are all the way across the screen, just EX Thunder Knuckle in for a free Ultra.

Its also good for people that like to charge up a Focus Attack and then dash away at the last minute. It doesn't matter if they tried to dash as long as you started your EX Thunder Knuckle motion, it will break their armor and free Ultra or combo.