I don't think they are, but with the Red and Blue Orbs...
Yeah, my brother and I were just talking about it today.
Maybe the Red and Blue Orbs are the mega stone. To
Mega evolve a pokemon you have to have a strong bond
with that pokemon and the stone. Well, in Sapphire you
got the Red Orb and in Ruby you got the Blue Orb.
So maybe the Orbs are their mega stones but we could
never use them because we never got the orb for that
legendary of that version.