Answer 1

They wanted it like that. Maybe, they made it a way so you can tell if someone hacs or not. If you see someone with a shiny zekrom/reshiram, you know for a fact that they hack and you shouldn't trade with them. That's just a theory and truely just game freak knows.

Answer 2

GameFreak shiny locked them, so you wouldn't waste your time by trying to catch them, and begin to play the game instead.
It's just a theory.

Answer 3

I think that GameFreak wanted people to try and divide up the awesomeness of strong Pokemon (Zekrom/Reshiram) and awesome Shiny Pokemon (any other Pokemon). Besides, would you rather have a weak shiny Pokemon or a super strong none-shiny Pokemon?

Comments

Well, in ingame, Id have weak shiny pokemon :D