Say that Shedinja would have the a normal spread of HP, it would be a little to HP thanks to it's ability in Wonder Guard that makes it rather impervious. To balance it out Game Freak gave it 1 HP so that it would be harder to use making it more challenging. It would be a Pokemon of godly presence that would make Arceus look like a Pun. Being able to take hits AND avoid them is just too much to ask for for even know it can be very annoying to take down Shedinja if you lack a few Pokemon or at least one Pokemon that can hit it supereffectively, induce it with burn toxic. Without Hail and or Sand it is impossible to bring it down. Should it have enough HP it would be able to pass down Sword Dance for entire team. With such an ability the entire metagame will become unbalanced.
