> They are the mascot of the games since G/S/C. They are ment to be powerful and play a role in the game's story-line. There might be a few more legendaries, depending on what game you play. However, still, they are important to their game alone.
> They are rare Pokemon found usually when you first step foot into the grass or while playing during the game's story-line. Shinies are usually harder to find, unlike most legendaries. They can also be very unpredictable, popping up at the most unintended times, which might cause players to rage when they have no PokeBalls or when it faints. However, unlike legendaries, it doesn't matter what game you're from, you'll have a chance to encounter one. When I say encounter one, I mean SEARCHING FOR THEM. Legendaries, however, stay still in one spot or whenever roaming is done, go to a specific location.
However, it make's it fair enough to put ONE legendary while providing as many shiny Pokemon as possible. Because everyone is somewhat like: "Shiny > Legendary" or "Shiny < Legendary." So it make sense, right?
TL;DR: It's just was GF decided, and they'll stick with it.