It's used in multiples of 3 to keep things streamlined and easier to keep track of, you know that you only need to check if the unit is dead every 3 wounds, it also works together with the Deadly rule to keep things "aligned". Generally a hero or large infantry unit will have Tough(3), a tank or monster will have Tough(6) and something really heavy will have Tough(9).
The tweaker in me says, "There's another knob to adjust here! Look how much we could vary models!" And while I appreciate simplicity, I don't see having multiples of three taking away a significant mental burden.
But the system doesn't feel broken in any significant way, so I'm good. I would like a few tweaks, like adjusting Defense here and there. For example, my archers have the same armor as the rest of my elves, and the elves with spears also have shields while the sword elves don't. But somehow, with these heartbreaking problems, my games have still been fun!